[gmx-users] molecule type

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 9 20:27:12 CEST 2011

Justin A. Lemkul wrote:
> 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.

Posting whatever topology you're using for nitrogen would also be helpful.



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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