[gmx-users] number of molecules generated during pdb2gmx

[Hyunjin Kim]

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.

Thanks for your help.


Hyunjin.