[gmx-users] error with changing pdb file

Justin A. Lemkul jalemkul at vt.edu
Thu Dec 17 21:31:23 CET 2009

ksm tprk wrote:
> I changed pdb file after that I generated topology file.

It appears you are relying on grompp to figure out what parameters should be 
used for these angles, and apparently, given these atom types, there are no 
default values available in the force field you've chosen to use.  So either 
specify parameters manually or use a different force field.

If you need further advice, it would be useful to know the force field you're 
trying to use and see the problematic lines of the topology alongside the 
modified coordinate file.



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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