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
--
========================================
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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