[gmx-users] missing topology file adn creating a new one

[Justin A. Lemkul]

sreelakshmi ramesh wrote:
> Dear all,
>               i am doing a sampling method and in a stage of completion 
> But unfortunatelymy topol.top file is missing and am really helpless .i 
> cant continue the simulation.i have the tpr file adn pdb file at last 
> step.i tried to create the top file from
> 
> *g_x2top -f beta_md17.tpr -o topol.top -ff select*
> when it prompts for a force field i selected charmm27 which is what i 
> used for the simulation it give me the following error
> Reading file beta_md17.tpr, VERSION 4.5.3 (single precision)
> Reading file beta_md17.tpr, VERSION 4.5.3 (single precision)
> 
> -------------------------------------------------------
> Program g_x2top, VERSION 4.5.3
> Source code file: g_x2top.c, line: 505
> 
> Fatal error:
> No or incorrect atomname2type.n2t file found (looking for charmm27.ff)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> 
> i* tried to use pdb2gmx as well
>  pdb2gmx -f  2.pdb -o 2.gro -p topool.top *
> End terminus GLU-56: COO-
> Opening force field file 
> /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/aminoacids.arn
> Opening force field file 
> /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/dna.arn
> Opening force field file 
> /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/rna.arn
> Checking for duplicate atoms....
> Now there are 16 residues with 247 atoms
> Chain time...
> Making bonds...
> Number of bonds was 250, now 250
> Generating angles, dihedrals and pairs...
> Before cleaning: 649 pairs
> Before cleaning: 654 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...There are   14 cmap torsion pairs
> There are  654 dihedrals,   35 impropers,  444 angles
>            640 pairs,      250 bonds and     0 virtual sites
> Total mass 1860.928 a.m.u.
> Total charge -3.000 e
> Writing topology
> Processing chain 2 (3 atoms, 3 residues)
> There are 0 donors and 0 acceptors
> There are 0 hydrogen bonds
> Warning: Starting residue NA2139 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue NA2140 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue NA2141 in chain not identified as Protein/RNA/DNA.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
> 8 out of 8 lines of specbond.dat converted successfully
> 
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.3
> Source code file: resall.c, line: 581
> 
> Fatal error:
> Residue 'NA' not found in residue topology database
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> 

pdb2gmx is ill-suited for dealing with multiple molecules.  You haven't said 
what's in your system, but if it's something simple like a protein in water with 
ions, it's trivial to re-create a topology.  Just run pdb2gmx on the protein 
only, then manually add the missing water and ions to the topology.

If you're system is something more complex than that, then hopefully you've 
documented your procedure well such that you can reproduce it.  And don't let 
files go "missing" :)

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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