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

[sreelakshmi ramesh]

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
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