[gmx-users] warning: Problem with chain definition

[afsaneh maleki]

Dear All



I would like to run a GROMACS simulation with one organic molecule on
a gold surface. At first I want to provide topol.top file for gold
surface system with g_pdb2gmx command. I want to use oplsaa force
field. I modified files like *.rtp* , *.dat*, and *.itp**. *in a local
new.ff directory (subdirectory) in the work directory where I am
working.

I edited the *atomtypes.atp* file to include a new atomtype:

Opls_966    196.000



I edited *aminoacids.rtp* file:

 [ bondedtypes ]

[ AU ]

   [ atoms ]

Au   opls_966   1.0       0



I edited *ffnonbonded.itp *as

opls_966    Au   79    196.99     0.0    A 3.20000e-01    6.50000e-01



I edited *residuetypes.dat *(in /use/share/gromacs/top) with

AU     Ion

…………………………………………………………………..

My *Au110-3.gro *file (input) is:

Gold surface

 2400

    1AU     Au     1   0.203   0.143   0.143

    1AU     Au     2   0.203  11.174   0.143

    1AU     Au     3   0.203  10.608   0.143

.

.

.

………………………………………

I try to run the structure file with pdb2gmx command:

I obtained this *topology file*:

;       It was generated using program:

;       g_pdb2gmx - VERSION 4.5.5

;

;       Command line was:

;       g_pdb2gmx -f Au110-3.gro -p tt.top -ff select -o out-gro

;

;       Force field was read from current directory or a relative path -
path added.

; Include forcefield parameters

include "./new.ff/forcefield.itp"



[ moleculetype ]

; Name            nrexcl

Ion                 3



[ atoms ]

;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB

; residue   1 AU  rtp AU   q +1.0

     1   opls_966      1     AU     Au      1          1    196.998   ;
qtot 1



; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif



[ system ]

; Name

Gold surface



[ molecules ]

; Compound        #mols

Ion                 1



But get me this *warning:*



Processing chain 1 (2400 atoms, 1 residues)

Warning: Starting residue AU1 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

Checking for duplicate atoms....

Now there are 1 atoms. Deleted 2399 duplicates.

Now there are 1 residues with 1 atoms

Making bonds...

No bonds

Generating angles, dihedrals and pairs...

Making cmap torsions...There are    0 dihedrals,    0 impropers,    0 angles

             0 pairs,        0 bonds and     0 virtual sites

Total mass 196.998 a.m.u.

Total charge 1.000 e

Writing topology

………………………….

Also I got .gro file (*output*) that contains one atom instead of 2400
atoms!!

*The question is:* How to remove this warning to get proper topology
file? Also, I changed AU as protein in *residuetypes.dat *file but I
obtained again this warning*.* Do I have to edit esiduetypes.dat?



Thank you in advance for any help

Afsaneh