How to do a transition state search using hybrid QM/MM (specifically Amber and Gaussian) ?

Hello,

I'm working on a structure with about 200 atoms. It is important for me to freeze a significant part of it for the time of optimization so that the arrangement of the given atoms with each other does not change. I tried to use "-1" before the symbol of atoms to be frozen, but unfortunately during the optimization the whole structure "began to move".

There are too many atoms and bonds to freeze them with the "redundand coordinates" option, hence my question how can you do it?

I care that during the optimization only a few atoms move, which are not connected to the main structure, which is frozen?

I am trying to run a QM/MM in Amber on a protein-ligand system. I have looked for tutorials but they don't explain a few things such as how to heat your system and equilibrate it before MD.

Then there are errors in output files. I have run the questions in the list and applied the changes, but the errors still remain. I would appreciate if someone could share their experience on running these for protein-ligand systems.

Thank you.

I want to perform a protein-ligand MD simulation using Amber. I have generated ligand frcmod, lib, rst7, and prmtop files. Then, I loaded my complex file, which contained the ligand and protein in water (generated using Packmol-memgen). However, when I tried to save the rst7 and prmtop files for the complex, I encountered this error: 'FATAL: Atom .R<***> does not have a type.' I've attempted to resolve this issue multiple times, but it keeps happening. I followed the tutorial exactly as outlined on the AmberMD website ('Simulating a pharmaceutical compound using Antechamber and the Generalized Amber Force Field'). Surprisingly, the problem persists. even though I tried to use the same molecule, protein, and files provided on the website to check out if there were any problem with my own files and again i ended up with same problem. Can anyone help me figure this out?"

Hi guys,

I am trying to optimize two semiconducting CNT molecules by using Gaussian 16.

My goal is to calculate interaction energy of the two CNTs.

The total number of atoms in the system is ~ 360.

Attached is the Gaussian input file.

(The molecular structure from the file is distorted because the optimization is ongoing.)

However, it has been about 2 months using 68 cores but it is not optimized yet.

I thought that it would take forever, so needs an approximation.

I freeze one of the two CNTs and the other remains free, and am still calculating it (refer to the attached file).

Hey all,

I am working with Gaussian 16 program package. For one of my geometry optimization calculations more than 100 geometry cycles runs are required. But even when I am including the tag "opt=(maxcycles=150)" in the input, it runs only up to 100 geometry cycles. So, please suggest the ways to increase the number of geometry cycle runs.

Your suggestions would be appreciated.

Thank You!

I seem to be consistently producing link 9999 errors during a TS search of a structure I generated from a mod-redundant scan geometry. As an example, I scan geometry modifying the bond length (fundamentally the position of the hydrogen) of hydrogen coming off a protonated water molecule (first frame) and finally bonding to oxygen of a carbon based molecule (e.g. enolization of the carbonyl group in glucose). I take the scan geometry of where the hydrogen is halfway between both molecules, and there is a slight adjustment of the O=C double bond (as this will change to a single bond upon associating with hydr0gen HO-C). Note: During the scan geometry, there are no major changes to the over all structure e.g., big steric clashes causing a large dihedral rotation of part of the glucose.

I have then tried a couple of basis sets.

# opt=(calcfc,ts) wb97xd/3-21+g* scrf=(solvent=water)

# opt=(calcfc,ts) wb97xd/6-31+g(d,p) scrf=(solvent=water)

With the smaller basis set I was hoping to approximate a TS structure and use it as a starting structure for a larger basis set. But in either case I produce the error:

Error termination request processed by link 9999.

Error termination via Lnk1e in /usr/local/g09/l9999.exe at Wed May 21 19:31:46 2014.

With the last optimisation step looking like this:

Item Value Threshold Converged?

Maximum Force 0.086348 0.000450 NO

RMS Force 0.014307 0.000300 NO

Maximum Displacement 0.874616 0.001800 NO

RMS Displacement 0.240702 0.001200 NO

Predicted change in Energy=-1.075204D-02

Optimization stopped.

-- Wrong number of Negative eigenvalues: Desired= 1 Actual= 4

-- Flag reset to prevent archiving.

Any ideas what I can do to rectify this problem. It is becoming a bit of a habit of Gaussian to kick out these errors every time I try a TS using a frame from mod red scan bond length.

I have now turned to QST3 using the first, last and intermediate scan step to determine my TS.

One of my coordination compounds calculations had the following error in Gaussian 09. Error termination in NtrErr: NtrErr Called from FileIO. Does anyone have an idea how it can be resolved?

Greetings,

In these days i'm trying to optimize the geometry of a polynuclear complex using G09 with B3LYP and 6-31++G(d,p) basis set (commands bellow). But at the end of 7th day of computation, i had a bad message:

(...)

EnCoef did 3 forward-backward iterations

Restarting incremental Fock formation.

Restarting incremental Fock formation.

Restarting incremental Fock formation.

Restarting incremental Fock formation.

Restarting incremental Fock formation.

Restarting incremental Fock formation.

>>>>>>>>>> Convergence criterion not met.

SCF Done: E(RB3LYP) = -4724.56420437 A.U. after 129 cycles

NFock=128 Conv=0.31D-07 -V/T= 2.0040

Convergence failure -- run terminated.

Error termination via Lnk1e in C:\G09W\l502.exe at Sun Mar 29 18:34:42 2020.

Job cpu time: 7 days 7 hours 17 minutes 52.0 seconds.

File lengths (MBytes): RWF= 369 Int= 0 D2E= 0 Chk= 46 Scr= 1

It took so long to failure. Can i continue this job using my checkpoint file? Is it worth continuing or should i start a new job?

command (first line)

#n B3LYP/6-31++G(d,p) Opt Pop=(Reg, Orbitals=9) Formcheck