[gmx-users] warning: Problem with chain definition

[Justin Lemkul]

On 8/7/19 6:57 AM, afsaneh maleki wrote:
> 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!!

I can't tell from the formatting of the email, but perhaps something is 
wrong with the line endings or format of the .gro file you're supplying.

> *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?


The warning is of no consequence. It is useful when you have a 
heterogeneous system (e.g. protein-ligand) where it can be more 
challenging to generate a topology. Warnings are advisory, errors are 
actual problems.

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================