[gmx-users] molecule type

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 9 20:24:54 CEST 2011

sarah k wrote:
> dear Justin,
> I should appreciate your guides in this period. They're really helpful 
> but again, I have some problem:
> I started over, several times as you suggested. I replaced the name of 
> SOL with N2. The problem of coordinates was solved by manual addition of 
> #N2 molecules to topol.top each time. But this error appears:
> Program grompp_d,
> Source file: topio.c, line: 587
> Molecule type 'N2' contains no atoms

Be sure your naming is consistent - the [moleculetype] and whatever residue(s) 
that are part of it are separate concepts.

> I checked the program of topio, grompp, and etc but I couldn't find SOL 
> molecule type to know how I can fix it. Would you please give me an 
> idea? Is gromacs able to simulate in non-aqous condition?




> Cheers,
> Sarah K.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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