3rd Jun, 2015
Indian Institute of Science
Question
Asked 28th May, 2015
Any step by step guidance for gromacs?
Hi,
Anyone can tell me how to add manually residues to topology ,when i use server im getting for optimised structure only.
please help me how to get all the parameters required to define topology,atoms,atomyptes dihedral,improper bonds etc
Most recent answer
Hi Umadevi
Structure got from the server is optimized ,it is not usable
Popular answers (1)
If you want go for simple dynamics of homology modeled protein structure to energy minimizing and confirmation stability, there is a basic protocol/steps described at Rizzo Lab Wiki (follow the link).
For mdp parameters you can reference the Gromacs MDP option (follow the link).
To add new residue to topology follow this steps:
#Adding a new residue:-
If you have the need to introduce a new residue into an existing force field so that you can use pdb2gmx, or modify an existing one, there are several files you will need to modify. You must consult the manual for description of the required format. Follow these steps:
Add the residue to the .rtp file for your chosen force field. You might be able to copy an existing residue, rename it and modify it suitably, or you may need to use an external topology generation tool and adapt the results to the .rtp format.
If you need hydrogens to be able to be added to your residue, create an entry in the relevant .hdb file.
If you are introducing new atom types, add them to the atomtypes.atp and ffnonbonded.itp files.
If you require any new bonded types, add them to ffbonded.itp.
Add your residue to residuetypes.dat with the appropriate specification (Protein, DNA, Ion, etc).
If the residue involves special connectivity to other residues, update specbond.dat.
Note that if all you are doing is simulating some weird ligand in water, or some weird ligand with a normal protein, then the above is more work than generating a standalone .itp file containing a [moleculetype] (for example, by modifying the .top produced by some parameterization server), and inserting an #include of that .itp file into a .top generated for the system without that weird ligand.
#Modifying a force field:-
In GROMACS 4.5 and later, modifying a force field is best done by making a full copy of the installed forcefield directory and residuetypes.dat into your local working directory:
cp -r $GMXLIB/residuetypes.dat $GMXLIB/amber99sb.ff .
Then, modify those local copies as above. pdb2gmx will then find both the original and modified version and you can choose the modified version interactively from the list, or if you use the pdb2gmx -ffoption the local version will override the system version.
(Source: Gromacs Online Manual)
6 Recommendations
All Answers (12)
Parametrization protocols vary depending on which force field you're using. The implementation of the parameters is fairly straightforward, just see Chapter 5 of the GROMACS manual. The hard work is in obtaining the parameters, for which you'll have to refer to the primary literature for your chosen force field.
4 Recommendations
If you want go for simple dynamics of homology modeled protein structure to energy minimizing and confirmation stability, there is a basic protocol/steps described at Rizzo Lab Wiki (follow the link).
For mdp parameters you can reference the Gromacs MDP option (follow the link).
To add new residue to topology follow this steps:
#Adding a new residue:-
If you have the need to introduce a new residue into an existing force field so that you can use pdb2gmx, or modify an existing one, there are several files you will need to modify. You must consult the manual for description of the required format. Follow these steps:
Add the residue to the .rtp file for your chosen force field. You might be able to copy an existing residue, rename it and modify it suitably, or you may need to use an external topology generation tool and adapt the results to the .rtp format.
If you need hydrogens to be able to be added to your residue, create an entry in the relevant .hdb file.
If you are introducing new atom types, add them to the atomtypes.atp and ffnonbonded.itp files.
If you require any new bonded types, add them to ffbonded.itp.
Add your residue to residuetypes.dat with the appropriate specification (Protein, DNA, Ion, etc).
If the residue involves special connectivity to other residues, update specbond.dat.
Note that if all you are doing is simulating some weird ligand in water, or some weird ligand with a normal protein, then the above is more work than generating a standalone .itp file containing a [moleculetype] (for example, by modifying the .top produced by some parameterization server), and inserting an #include of that .itp file into a .top generated for the system without that weird ligand.
#Modifying a force field:-
In GROMACS 4.5 and later, modifying a force field is best done by making a full copy of the installed forcefield directory and residuetypes.dat into your local working directory:
cp -r $GMXLIB/residuetypes.dat $GMXLIB/amber99sb.ff .
Then, modify those local copies as above. pdb2gmx will then find both the original and modified version and you can choose the modified version interactively from the list, or if you use the pdb2gmx -ffoption the local version will override the system version.
(Source: Gromacs Online Manual)
6 Recommendations
Thanks
i am defining required items and encounter with an error
can you tell me what it means?
""Atom HN in residue LIG 2 was not found in rtp entry LIG with 110 atoms
while sorting atoms.
For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.""
You'll need to provide the LIG .rtp entry and the input coordinates. It's hard to diagnose the problem without that information.
This file won't work as a pdb2gmx input because the atom names aren't unique. You also need to provide the text of the .rtp entry; I can't diagnose the problem at all without it. The coordinate file alone is not enough.
i made the structure using Chemcraft softwares and using Avogadro software i got the
PDB file..
and i defined rtp entry by the data obtaining from Avogadro software
here is the rtp entry i made
OK, you need unique atom names. Your .rtp also does not specify bonds, which are mandatory. Of course now you will see the problem - how do you define the bonded connectivity unambiguously? You can't unless you correct both the coordinates and the .rtp file, otherwise there is no way to tell that the first C is different from the second C, etc.
So your saying the direct conversion using software Avogadro wont work and i have to add coordinates and rtp entry manually??
if it so is there any guidance material i can get for doing both?
You can try it using prodrug server or some other topology creater. it will be use ful for ur simulation
PRODRG produces topologies with many errors; I do not recommend it. A lot of software programs produce PDB files that are sub-standard; therefore, no, a direct transfer from Avogadro to GROMACS will not work without many correction of the issues in the coordinate file.
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