Hydrogen Bonding - Science topic

Dear friends,

I am a researcher who study on oxides and I am interested in hydrogen bond analysis.

Unfortunately, the most software I can find to perform hydrogen bond analysis only support PDB file. But my common file is XYZ format.

I try ASE and turn my XYZ file into PDB format.

Buy when I load such PDB file in MDtraj python modules, I find the Topology always contain no bonds!

Here is my code.

python will return :<mdtraj.Topology with 1 chains, 1 residues, 96 atoms, 0 bonds>

since no bonds, there is no way to continue to do hydrogen bond analysis.

How can I generate bonds between my interested atoms?

Any advice will be appreciated !

Hi everyone, I’m analyzing the 1H NMR spectrum of polyvinyl alcohol (PVA) on a 600 MHz NMR instrument using DMSO-d6 as the solvent. I found that the integration ratio between the alpha proton (H-C(OH)) and the methylene protons on the backbone is 1:2.68, rather than the expected 1:2 ratio. I’m curious about the underlying reasons for this discrepancy. Could factors like relaxation effects, hydrogen bonding in DMSO-d6, or other environmental interactions be influencing the integration values for the alpha proton?

If anyone has encountered similar issues in PVA, or if there are known studies explaining this phenomenon, I would greatly appreciate your insights.

Thank you!

Dear ResearchGate community,

I have recently conducted two separate 100 ns molecular dynamics simulations using GROMACS, each involving a small molecule. My analysis of hydrogen bonding patterns has revealed an unexpected observation: zero hydrogen bonding and an unusually large number of pairs within 0.35 nm. For instance, at a specific time point (e.g., time = 1.90108e-33 ns), the number of hydrogen bonds reported is >1110000000. I would like to know about such variations and how should I fix it, and if anyone has insights into the potential implications of this observation. I appreciate any feedback or experiences you can share on this matter.

; Include forcefield parameters

#include "./charmm36-mar2019.ff/forcefield.itp"

; Include ligand parameters

#include "crx.prm"

Thank you

Hello everyone,

I am currently working on a molecular docking project and have obtained results that I need help interpreting. I would greatly appreciate any guidance on how to analyze these results effectively, including insights about RMSD (Root Mean Square Deviation), binding affinities, binding poses, hydrogen bonds, and the amino acids involved in these interactions.

Any resources, tips, or personal experiences you could share would be immensely helpful!

Thank you in advance for your assistance!

Dear researchers,

Very recently, I have downloaded the last version of IGMPlot, version 3.08. I found some new descriptors included in this very nice, complete, and versatile version. One of newly proposed descriptors is "qg" which makes 2-D plots colored based a given scale ranging from 1 (blue color) to 4 (red color). Please let me know the exact and straightforward meaning of these numbers and colors. Indeed, what is the practical usage of "qg" index? or, what is its interpretation when a given inter- or intra-fragment interactions is analyzed? I cannot understand what concept should be taken into account when a 2-D plot of delta_g_inter versus sign (lambda2*Rho) is colored from blue to red (from number 1 to 4). What practical information one can obtain depending on the color type of a given picke. For instance, a taller picke (a larger delta_g value) means a stronger interaction but what statement should be provided for a smaller (blue) or greater (red) value of "qg"? In advance, too many thanks for any help.

Best,

Saeed

Solvent : HYDROCHOLORICACID,

Eps = 78.000000

Eps(infinity) = 0.00000

RSolv = 0.000000 Ang.

Molar volume = 0.000000 cm**3/mol

Thermal expansion coefficient = 0.000000 K**-1

Absolute temperature = 298.150000 K

Numeral density = 0.000000 Ang**-3

Hydrogen bond acidity = 0.000000

Hydrogen bond basicity = 0.000000

Surface tension at interface = 0.000000 (cal/mol)Ang*-2

Carbon aromaticity = 0.000000

Electronegative halogenicity  =   0.000000

Numerous studies have reported the positive effects of hydrogen-rich water (HRW) on various physiological parameters, leading to multiple health benefits. Additionally, HRW has shown to be highly efficient in extracting various components from plants, such as phenolics, flavonoids, antioxidants, anthocyanins, pigments, and more.

One of the reasons behind HRW's different activities is believed to be the modification of the physical and chemical structure of water by dissolved hydrogen. In simpler terms, the question arises: Does dissolved hydrogen in water affect hydrogen bonds, and if so, how does this effect behave with respect to the pH value?

Thanks

The nuclear magnetic F spectrum (19F NMR) shifts towards lower or higher fields when hydrogen bonds are formed between H atoms and F atoms?

What is the nature of H-bonding in GROMACS ? Is it primarily electrostatic , or does it calculate the number of H-bonds based on the angle and distance criteria?

(I used the CHARMM36 force field for my MD simulation)

Pyroteccol and hydroquinone are two phenolic isomers that differ in the position of the hydroxy group.

Hydroquinone is a non-polar compound and pyrotechol is a polar compound, but both dissolve in many solvents due to hydrogen bonding.

I have been trying to learn QTAIM analysis for understanding hydrogen bonding interaction .

I have basic knowledge of Gaussian software and Density functional theory.

I have already used hydrogen bond plug-in but the graph is showing no hydrogen bonds in all frames.

Can XPS detect hydrogen bonds？ Whether XPS results are firm evidence of hydrogen bonds？

i have silk fibroin powder i want to dissolve it in water without adding LiBr or any other dissolving agent how its possible to dossolve in water. if dissolve it at 4C is it possible.

i need to break down its hydrogen bonding then i will be dissolved.

need your kind suggestion.

Hello dear Quantum Chemists, I would like to run a metadynamics simulation for a hydrogen bonded complex using orca software. I would like to get the delta_G for the hydrogen bond. Is there anyone here who has some experience with running metadynamics simulations? Please, I need some help with the input format. Thank you.

Dear all

Post docking I am not able to see any hydrogen bond interaction in my complex in ligplot. While when I visualised the same complex in DSV studio able to see two three conventional hydrogen bonds. Can you please help me is there any way to enhance hydrogen bonding during docking.

And is there any way to visualise the conventional H bond interaction in ligplot which were visible in DSV studio.

Hydrogen bonding occurs when a hydrogen atom forms a covalent hydride with an atom of large electronegativity and small radius, which is almost protonated due to the strong shift of the shared electron pair between the atoms. This hydrogen atom can also have an electrostatic attraction with another atom that has a large electronegativity and contains a lone pair of electrons.

When characterized by FTIR and XRD, a red shift of the peak of the group may occur when hydrogen bonding occurs, but I have found that this phenomenon is often not apparent in actual tests.

In X-ray diffraction (XRD) characterization, the occurrence of hydrogen bonding causes self-assembly, which increases the intensity of the diffraction peaks on the crystalline surface, but I have read in some of the literature that co-mingling also disrupts the crystalline structure, which reduces the intensity of the diffraction peaks。

I want to determine if there are acid-base reaction or just hydrogen bond interaction between 2 organic molecules by Gaussian software. Can anyone help me on this problem? Thank you in advance.

Hello,

Can anyone can help me how can I use" multicomponent hydrogen bond propensity" feature in mercury and relate them to python in order to export data if there any confomer have passed the cocrystal or not?

thanks alot for your time.

Can Anybody help me on how to find Hydrogen-Bond occupancy of RNA unfolding. Which software can be used for the same.

I know that FTIR spectroscopy is usually used to detect the vibrational characteristics of molecular bonds (bending, stretching, etc.) in the IR region. I also know that, for water, information about hydrogen bonding can be determined based on how these bending/stretching vibrations are shifted/modified (e.g., image attached, from J. Chem. Phys. 134, 164502 (2011)).

Besides this, I would like to know if FTIR can be used to detect hydrogen bonds directly, as opposed to sensing them based on modifications to other bonds. From my understanding, hydrogen bond strengths in water may vary in the range of about 1800 cm-1 (e.g., liquid water) down to roughly 1000 cm-1 (e.g., for water dimers or other clusters in the vapor state).

I assumed incoming radiation matching the bond strength could be absorbed and break/dissociate the H-bond, in which case an absorbance peak would be visible. But I haven't found any work in the literature that does this, so I assume it's not valid. If the H-bond energies are in the IR range, why can't FTIR be used to detect them?

Thanks!

Andrew

I have been trying to identify correlations between assay specific EC50 values to in silico data (binding free energy, residue specific hydrogen bond occupancy, MM/PBSA energy values) for a range of compounds and their target receptors. Since they are different parametric dataset, I am looking forward to a more non-linear correlation approach. However, state-of-the-art approaches like KendallTau, Cannonical Correlation is unable to explain any variability or likelihood among the in silico and in vitro data. Dimensionality reduction method also does not explain much variability. This could be because I am trying to compare two different domains of data.

I would like to know if there is any established method of comparing such datasets.

Dear researchers and scientists

I did a partial docking experiment to learn the basics of using an internet server. (Seamdock). Two ligands, the first is known to inhibit the target protein and the other to test. Both gave similar results of docking affinity. But the first ligand showed hydrogen bonds with the macromolecule, while the second has only hydrophobic interaction. How do I judge these results? I will attach the files.

And if there is a direct forum for specialists, please guide me

MHBS should be a unitless quantity?

I am mixing water and DES with different concentrations

Tcl script is needed.

I appreciate any help you can provide.

gromacs command

I am adding the Graph result below. The whole trajectory run was 20 ns. is there any particular threshold value for H-bond?

What's the β-pair of β-sheet?Is one pair amino acid?Or is short peptide chain?

Could anyone suggest any web server/software/ any other method which identifies or lists all the salt bridges and hydrogen bonds present in a protein structure.

Given a PDB structure file, I want to find interactions between protein residues, particularly I want to know if the residue R123 interacts with the residue E145, and what kind of the interaction (e.g. salt bridge, VdW force or hydrogen bond?)

I have seen someone do it using All-atom Contacts (AaC), but is it only a method to validate the quality of structure? I'm confused.

In many researches, the mixture of MeOH and acetic acid (= 9 : 1 , for example) is commonly used, in order to remove the template molecular in molecular imprinted polymer (MIPs).

I wonder why this mixture solution is widely used, and what the meaning of this operation is.

I can imagine that the aim is to change the pH of slurry solution of MIP so that the structure of template molecular changes, and affinity and interaction between template molecular and monomer decreases.

But, I have a concern about my hypothesis.

In my research, I use 17β-estradiol (contains -OH) as a template molecular, MAA (pKa: about 4.6) as monomer. The interaction is related by hydrogen bond between "-OH of 17β-estradiol" and "-COOH of MAA".

If I take the pH condition of my reaction solution into consideration, I hypothesize that the lower pH leads to the more ratio of molecular form of MAA, so that the hydrogen bond get stronger.

However, the mixture of MeOH and acetic acid (the lower pH than the solvent of reaction solution, toluene) is used for removing molecular, according to the research which I refer to.

Are my hypotheses correct or incorrect?

I am having a solid liquid system. The system has a solid liquid interface along the Z-direction. I wanted to study the evolution of hydrogen bonds in the solid phase over time. So I decided to use gmx hbond.

I looked into the internal code for hbond analysis and found that it has taken into account periodic boundary conditions. However, my system is clearly not periodic along the Z-direction. So is it correct to use gmx hbond ??

Hello,

I am running a VMD simulation and using VMD software to analyze hydrogen bonds, but I want to study electrostatic interaction. I would like to have a graph number of bonds through time. I don't know if I'm in the right place to ask, but would you know how to obtain this graph for the electrostatic bond? I tried to find answers on the internet but couldn't find any.

Thank you so much for your help.

Alix

Hello everyone,

I tried to dock a ligand to a molecule using AutoDock software with a blind docking method. My ligand is an under-investigated small-drug molecule and the protein interactions of the ligand is not known. From my docking results the binding energy for the molecules I investigated was found as -5.78, however there was no hydrogen bonds formed between these molecules. Can I assume that these molecules are docked or how can I check the reason why hydrogen bonds weren't formed?

Additionally, is there any way anyone can recommend to screen the proteins interacted with a ligand whose proteins interactions weren't studied?

Sorry for the inconvenience,

Thanks in advance.

Mervenur

Polymer Flooding

1. For a reservoir with formation damage, if we go ahead with polymer flooding, won’t the polymer molecules get blocked – particularly – by the smaller pore sizes?

2. If the polymer molecules get blocked in smaller pore sizes, where and when will it happen from the injection well or the core-inlet?

3. If the polymer molecules get blocked in smaller pore sizes, to what extent, further transportation of polymer molecules – into the reservoir – horizontally – away from the injection well – gets influenced?

4. If the polymer molecules get blocked in smaller pore sizes, to what extent, polymer molecules get dispersed and diffused (on top of its expected advective transport) as a function of pore-sizes – during its transportation – away from the injection well?

5. Whether the shear and pull forces associated with the polymers will get influenced/altered – nearer to the injection well itself?

In such cases, will it lead to the partial or full destruction of polymer structures?

In case, if the polymer structure gets destructed, then, how will it do the intended job of enhancing the water viscosity?

Further, whether, viscosity reduction - would lead - to an enhanced adsorption (and sometimes absorption as well) of polymer molecules to the grain surfaces and thereby further making the polymer flooding process weaker?

OR

would it require an enhanced water saturation as well – for the polymers to retain their enhanced viscosity?

6. Feasible to get the details of reduction in water-phase permeability – resulting from polymer retention in pores – at the field-scale?

7. In a real field scenario, whether polymer molecules retain to have a strong hydrogen bonding with water molecules – particularly – away from the injection well or the local pore-size distribution play a crucial role?

8. Whether the adsorption of polymer molecules onto the surfaces of the solid rock grains would really aid the flow of oil comfortably in the absence of significant frictional resistance?

If it is so, then, polymer flooding enhances the sweeping not only volumetrically or macroscopically but also microscopically?

***

Dear All,

In vasp, I would like to calculate the non-covalent interactions (NCI), more precisely the amount of hydrogen bonding, van-der waals interactions, and steric repulsions in which the H2O molecules are involved. I need to see their magnitude. Could you recommend any tools/program?

In advance, thanks a lot for all help.

I am trying to calculate hydrogen bonds between protein and ligand but i am unable to calculate per-residue hydrogen bonds using gmx hbond command of gromacs.

Please suggest me a way to do so.

I'm doing molecular dynamics simulation to study the effect of mutation towards thermostability of an enzyme. After doing some analyses using VMD, I found that mutant is more stable than wild type, new hydrogen bonds and salt bridges are formed. VMD told me that new hydrogen bond are formed at the residue that I have mutated before, with % occupancy higher than 50 %. I've read that the higher % occupancy of hydrogen bond means higher stability of hydrogen bond during simulation. I also read some articles, websites and journals, but none of them make me understand about hydrogen bond occupancy. Would you like to tell me, or suggest me, where I can read about hydrogen bond occupancy ? Thank You

Dear Gromacs users，

I want to know the Hbond occupancy .Now I can only use VMD to calculate the final hydrogen bond occupancy rate of the simulated environment, but I want to understand the change of this hydrogen bond occupancy rate over time. What should I do? Please help me to provide some methods。

Hello everyone,

I docked a protein with a ligand that contains bromine "Br", I got a very good result of binding energy, inhibition constant and number of hydrogen bonds (5H bonds) but I could not visualize the 2D diagram of interactions with the discovery studio, knowing that I have no problem with the autodock vina or with discovery studio. Is there anyone who can help me please!?.

Hello I did 100 ns simulation using GROMACS a protein protein complex ( chain A for antigen - chain B & C for antibody) now I want to calculate the number of hydrogen bonds. I select chain A and chain B, but it shows nothing. What i should select for selection 1 and selection 2?

I am optimizing the method of developing natural deep eutectic solvent by using different methods, molar ratio and water content. For heating and stirring method, I used 1:1 Choline chloride:1,2 propanediol. The combination does not form liquid either direct heating or in water bath up-to 2 hours. The temperature is below 100 degree C. I tried to add minimal amount of water (less than 50%). However, the combination does not form homogeneous solution. It only form clear homogeneous solution when I put more water (160%) and its stable at room temperature. My concern is some journals mention the excessive water content may disturb the hydrogen bonds between Choline chloride and 1,2 propanediol. I tried to rotavap to remove water content and it starts recrystallising again. I repeated the experiment by using total dried Choline chloride (freeze dried) after reading some suggestions from previous researchers that had similar issue that caused by wet Choline chloride. However, I obtained similar results 😢. May I have some other suggestions or opinions that may solve the problem? Thanks in advance

Hi researchers,

I have used Amber16 to run a molecular dynamics simulation of my protein system for 50 ns. After the production run was completed, I have generated an MD trajectory with 2500 snapshots which I further analysed using the Cpptraj program. The issue is, after doing a few analyses using cpptraj, the results were generated in the .DAT extension which I can only open in Excel. I analysed the dynamic cross-correlation of all atoms (DCCM), hydrogen bond analysis, Radius of gyration and all the results were generated in the .DAT extension (file format). Therefore, can anyone suggest to me how to change the result file format or what are the software, can be used to view the results generated by AMBER 16? If there is an option in AMBER to visualise this file format, then kindly do let me know as it will help me to progress my research.

Thanks, regards

~Priya

Is OH bending IR band in PVA is related to inter/intermolecular hydrogen bond? why does it disappear on blending with another polymer?

Can anyone suggest a suitable reference?

Hi all, I have used the below code for analyzing hbonds in my protein, but I am facing the error below. Please provide solution for this error?

python3 readHBmap.py -hbm hbmap.xpm -hbn rg.ndx -f md_0_1.gro -o occupancy.xvg -op pairs.dat -t 80 -dt 100

ERROR: Traceback (most recent call last):   File "readHBmap.py", line 295, in <module>     startingLine,framesLine,numberFrames,numberHbonds=readFiles().hbmap(hbmap,inputHbmap)   File "readHBmap.py", line 208, in hbmap     numberFrames=int,framesLine[0] TypeError: 'map' object is not subscriptable

I search for the forces acting on the adsorption from water of an insoluble particle onto polymer surface. I found that the intermolecular forces that governs the adsorption in water are the hydrogen bonding and van der waals forces. My question is about the effect of the hydrogen bonding (in water medium) on insoluble particles in water?

Hello,

I'm currently making a life cycle assessment for a liquid hydrogen tank.

One of the materials considered is a carbon fibre reinforced PEEK.

However, there is not a lot of data about the environmental impact of the polymer. Indeed, the only article I have found is the one from Daniel GARRAIN (which served as a reference for the Idemat database).

(PDF) The environmental behaviour of PEEK as an innovative material in a new portable hydrogen fuel cell (researchgate.net)

If any of you have data about it, I would be interested in exchanging with you.

Regards,

I'm currently looking at the rheological properties of the polymer Xanthan Gum. focusing on its dynamic viscosity to be more specific. I'm assessing the effects of pH (ranging from 3.6 to 5.6, 0.4 increment, total of 6 pH's) on the dynamic viscosity of xanthan gum solution (dissolving xanthan gum powder into acetic buffer with equal ionic strength, concentration is kept at 0.04%).

Firstly, my viscosity data collected shows that, as pH increases from 3.6 to 4.0 then 4.4, the viscosity increases; but as I bring up the pH from 4.4 to 4.8, 4.8 to 5.2, then lastly 5.2 to 5.6, the increasing viscosity trend plateaus and the increase in viscosity is less significant compared to the 3.6-4.4 jump. At this range, does pH has an effect on the viscosity of xanthan gum based on its molecular configuration? Though some sources states that xanthan gum's viscosity remains stable and unchanged within the range of pH 3-12 at a high concentration like 1% not 0.04%, yet some suggest pH still plays an effect, though I'm not sure how on the chemical and molecular aspect.

A possible conjecture I can think of is the xanthan gum's order-disorder and helix-coil transition is affected by protonation. In figure 2, it demonstrates how electrolytes affect the structure of the polymer; in figure 3, it shows how at a state of a helical rod and no longer a random coil, it is capable to hydrogen bonds among each other. Hence, I'm wondering of pH plays an effect on it's structural transition, such that the increased intermolecular forces at the form of a helical rod would make it more viscous in solution.

Here are the resources I have used so far:

Brunchi, CE., Bercea, M., Morariu, S. et al. Some properties of xanthan gum in aqueous solutions: effect of temperature and pH. J Polym Res 23, 123 (2016). https://doi.org/10.1007/s10965-016-1015-4

I need to know a way to calculate the hydrophobic interactions between the protein and the ligand. in addition, I also need to do the same for the electrostatic interactions and hydrogen bonds. but the hydrogen bonds i can get from VMD easily. the goal is to make a graph like the attached one. any help is appreciated.

Hi all,

I am wondering if there are any good benchmarking studies out there testing the accuracy of B3LYP, DSD-PBEP86, or M06-2X functionals for NMR determination of intramolecular H-bonding. (My compound/drug is somewhat large: 4-anilino-6,7-ethylenedioxy-5-fluoroquinazoline. And I am looking at the rather rare NH---F bonding. (I must use DefT2ZVP basis set, as one of the R group constituents will eventually be Iodine. We are going through a series of halogens with increasing electron-withdrawing properties (σp>0).)

Thus far, I have read that B3LYP is rather ubiquitous, and very accurate for geometrical parameters. M0 functionals, however, appear to be good for non-covalent bonding determination.

"Experimental and theoretical DFT (B3LYP, X3LYP, CAM-B3LYP and M06-2X) study on electronic structure, spectral features, hydrogen bonding and solvent effects of 4-methylthiadiazole-5-carboxylic acid"

Hello!

I have a few questions related to molecular docking and its analysis. I used Ligplot+ to analyse my docking results.

To visualize hydrogen bonds in Pymol between a protein and the surrounding water molecules, I tried using "Action -> Find -> Polar Contacts -> Involving solvents", which shows hydrogen bonding between solvent molecules and protein and hydrogen bonding between different solvent molecules, making visualizing hbonds between just the solvent and protein very messy. Is there a way (that preferably does not involve writing a script) to display only the hydrogen bonding between the solvent and protein?

I encounter a similar problem in VMD, where I tried to create an HBond representation with the selected atoms as "protein or (water and within 3 of protein)"

Hi there,

I am a little confused about a few concepts that I would like elucidated. An article states, "This phenomenon can be rationalized by the fact that the NH proton becomes more acidic with increasing electron-withdrawing character of the 4’ substituent and thus more strongly hydrogen bonding."

Meanwhile, the process of determining if intra-HBs exist is given by another article, which uses hydrogen bond acidity and the formula:

Δδ = δ(DMSO) − δ(CDCl3)

and

A= 0.0065 + 0.133Δδ

"For NH compounds, if A > 0.16 the NH group is not part of an intramolecular hydrogen bond, and if A < 0.05 the NH group is part of an intramolecular hydrogen bond."

So, in this case, a LOWER value is indicative of stronger HBs.

I believe my confusion may be down to the fact that the first instance is looking at the NH proton, whilst the second is looking at the bond itself.

Indeed:

"...the overall hydrogen bond acidity of a molecule, A, and does not relate to any specific acidic group in a molecule. It is only a measure of the hydrogen bond acidity of a particular NH group if this is the sole acidic group in the molecule."

Let's say I take a snapshot from a GROMACS molecular dynamics trajectory and want to visualize which residues of the protein forms hydrogen bonds with the surrounding water molecules. I know this can be done using Pymol's "find polar contacts" tool, but since there's so many other water molecules in the solvent box, it's hard to visualize just the water molecules involved with hydrogen bonding with the protein. Is there any way I can remove water molecules not involved in hydrogen bonding with the protein and keep the ones that do? Thank you!

Hi all,

just reading through an article regarding intrabmolecular N-H...F bonding. This articles serves as one of the teaching pieces for my internship.

Just wondering how to calculate the ΔEint, as I cannot find it in my optimisation file. Do I need to perform NMR at this stage?

Cheers,

Joshua

As hydrogen bonding is one of the important parameter for shale hydration inhibition with water, what happens after this bonding?

like when clay mineral charges are neutralized by hydrogen bonds and cation exchange reactions between inhibitor and minerals, does the adsorption of inhibitor layer on shale surface count as swelling? Because it will somehow increase the size of original formation due to adsorption.

How to address this issue.

What are the differences between the hydrogen bonds formed in an alpha helix and those formed in beta shears?

I have docked the compound and got free energy _9kcal, however, no hydrogen bonds seemed to be formed with protein .can anyone guide the compound is docked?

I had followed the jerkwin tutorial for MD trajectory analysis, and i want to calculate the hydrogen bonds distance between each residues of my protein.

Hello.

which one have more hydrogenic bond,alpha helix or beta sheet?

iappreciate your comments.

I have a mixture of DMF and water in 300 K simulated with an OPLS-AA force field. The hydrogen bonds between oxygen atoms of DMF and H atoms of water have a very short length and it's around 1.26 Å. I know that H-bonds are typically < 3.5 Å but isn't 1.26 in the range of covalent bonds?

I want to know if that's possible or if there's something wrong with my force field parameters/charges?

The RDF curve of oxygen atoms of DMF around H atoms of water (H-bonds) is shown below.

Kind regards,

Ehsan

Dear colleagues researchers,

Could you help me with a problem in MD analysis using Gromacs?

I'm using Gromacs version 2021.4 now, and trying to analyze hydrogen bonds (using HbMap2Grace) with the command:

gmx hbond -f ../md_center.xtc -s ../md.tpr -n ../index.ndx -num hbond-lig -r -0.4 -hbm hbmap-lig -g hb-lig -life hblife -tu us

The program gives me the following error:

I've also tried it with version 5.1, 2018, 2019, 2019.6 and 2020, but all with the same problem.

P.S.: I don't think it's a lack of physical memory on my computer, cause there is enough storage space.

I mean for example

the hydrogen bonds formed in aspartic acid between the amino group and the carboxyl group are two hydrogen bonds?

I am Working on developing Schiffs Base - Transition metal Complexes Having -OH Group at Terminal Position leading to the formation of Hydrogen bonding ! However I I unable to get the crystal Structure for the same !! Would anyone give me some suggestions Please ? Although I have tried almost all the solvents like MeOH, EtOH, Acetonitrile , etc

Hi, I'm simulating a box with water and Li+ and Cl- ions and I'm trying to calculate the hydrogen bonds formed by the Cl- anion and the water molecules using the gmx hbond. The command I was using was:

gmx hbond -f .xtc -s .tpr -n .ndx -num -r 0.41 (O-Cl distance taken from Laage & Hynes, PNAS, 104, 11167-11172, 2007)

And the program gets back to me whenever there are no hydrogen bonds, I believe it's because the hbond only sees O and N atoms as acceptors. So I started adding the -contact flag that do not look for hydrogen bonds, but merely for contacts within the cut-off distance, and I use the command:

gmx hbond -f .xtc -s .tpr -n .ndx -num -r2 0.41 -r 0.3 -contact

however the contact values are higher than what I expected and I believe I cannot consider the contacts as hydrogen bonds. I'm not sure what to do and would like to know if anyone has any suggestions.

I am trying to correlate the IR spectrum and single crystallography data.

In single crystal IR spectra, I found some inter-molecular hydrogen bonds were stronger (from wavenumber shift), and I think the different hydrogen bond strengths are due to different crystal packing. (At least in single molecule quantum calculations, the -OH wavenumbers are mostly the same)

Is it reasonable that I run QM/MM based on the single crystal molecular geometries (.cif files) and calculate the -OH vibration (freq) to correlate with experimental IR data?

I am not familiar of how single crystal technician actually grab the .cif data, so I am wondering if the cif. files that I received are actually reflecting the molecular packing in real.

We're trying to obtain a computational model of a protein that has not been experimentally solved. There are no homologous proteins, and the best protein structure prediction tools available right now (i.e. RoseTTAFold, AlphaFold 2) failed to predict a folded structure.

However, we believe the protein is likely a beta helix (e.g. similar to PDB: 1EZG) due to its similar chemical properties with other common beta helical proteins, and we have a guess on which residues are involved in hydrogen bonding/beta sheets as well as what the overall beta helical structure of this protein might be like.

Are there any good tools for building a protein from scratch by hand? I tried using Schrodinger's "Build Peptide From Sequence" tool, but that requires specifying the psi and phi angles of each residue not involved in an alpha helix or beta sheet. This makes it extremely difficult to make sure the residues we expect are hydrogen bonding to line up correctly. If there is a tool that can build a protein and adjust each residue by hand, then lining up residues so hydrogen bonding is possible would probably be much easier. Are there any such tools, or are there better ways for building a protein from scratch? Thank you!

i am using auto dock. during the protein preparation i added the add polar hydrogen bond. when i went to save, it is showing error that the protein has 84 non bonded atoms

I am interested to know the hydrogen bond strength in ligand docking. Ligand is participating in Sulfur mediated hydrogen bond. I would like to calculate or find out the strength of the same. Kindly suggest me. Note: by using Schrodinger Material software