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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