[gmx-users] Invalid particle type

[Justin Lemkul]

On 8/9/19 11:09 AM, afsaneh maleki wrote:
> Dear All
>
> I generated topology.top file for Gold surface with g_pdb2gmx          -
> VERSION 4.5.5 using oplsaa force field as the following:
>
> ;           Command line was:
>
> ;           g_pdb2gmx -f Au110.gro -p 1 -o 1
>
> ;           Force field was read from the standard Gromacs share directory.
>
> ; Include forcefield parameters
>
> #include "oplsaa.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
>
> ; residue   2 AU  rtp AU   q +1.0
>
>       2   opls_966      2     AU     Au      2          1    196.998   ;
> qtot 2
>
> .
>
> .
>
> ; residue 2400 AU  rtp AU   q +1.0
>
>    2400   opls_966   2400     AU     Au   2400          1    196.998   ;
> qtot 2400
>
> ; Include Position restraint file
>
> #ifdef POSRES
>
> #include "posre.itp"
>
> #endif
>
>
>
> [ system ]
>
> ; Name
>
> gold surface (2400 residue)
>
>
>
> [ molecules ]
>
> ; Compound        #mols
>
> Ion                  1
>
>
>
> After that, I modified topology file hardly:
>
> # mols    1   to    #mols   2400    since I had defined 2400 residues.
>
>   I don’t know why g_pdb2gmx write one residue in part of [molecules]*?*

You should not do this if there are 2400 particles. pdb2gmx has written 
a single [moleculetype] for all of them. Your topology now specifies 
2400*2400 particles. The concept of a "molecule" in GROMACS has nothing 
to do with chemical features, only what you specify in an input file.

>
>
> When I try to run g_grompp, it failed with massage:
>
> *Fatal error:*
>
> *Invalid particle type 0.0 on line opls_966   Au     79   196.9940
> 0.0              3.20000e-01  6.50000e-01*
>
>
>
> I moved [atomtype] partition from ffnonbonded.itp to topology file before [
> moleculetype ], I again obtained this error.

You need to specify a particle type, e.g. A for atom. See existing lines 
for the correct syntax.

-Justin

>
>
> Any relevant idea is appreciated.
>
> Afsaneh

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

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

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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