[gmx-users] number of molecules generated during pdb2gmx

[Justin A. Lemkul]

Hyunjin Kim wrote:
> Hi,
> 
> I included a small organic moelcule using separating .itp and .rtp files
> in charmm36.
> If I ran pdb2gmx to generate top file, it generated properly.
> However, although I included 256 molecules, it still treated them as one
> molecule as follows:
> 
> 
> [ molecules ]
> ; Compound        #mols
> Orgainic             1
> 
> If I correct it manually, then it built the following error:
> -------------------------------------------------------
> Program grompp, VERSION 4.5.4
> Source code file: grompp.c, line: 523
> 
> Fatal error:
> number of coordinates in coordinate file (thf.gro, 3328)
>              does not match topology (thf.top, 851968)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 
> It looks 256 molucules are considered as one molecule. Can I treat them
> each residue as one molecule as the water case?
> I have searched for this on your web, but I can not find the proper way to
> fix this.
> 

If you have an .itp file already, running pdb2gmx is unnecessary.  Make a simple 
topology with a text editor, generically:

#include "forcefield.itp"
#include "molecule.itp"

[ system ]
my system

[ molecules ]
MOL 256

-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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