[gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 29 23:13:53 CEST 2012

On 6/29/12 4:44 PM, sreeta.g wrote:
> Hi Justin
> Thank you for your reply.
> However, when I am using the grompp command, the topol.tpr file is not being
> formed due to a fatal error. This fatal error is the cumulative of ' No
> default Ryckaert-Bell.' types for many atoms in the polymer chain.

And as I suggested before, you should investigate which lines are causing 
complaints to diagnose why grompp is failing.

> Also, regarding the comment on the atom types and atom names, I have tried
> Google searching to find the difference, but in vain.

An atom name is an arbitrary label.  An atom type is a designator that supplies 
various nonbonded parameters (listed in the [atomtypes] directive of 
ffnonbonded.itp.  The files you posted before seem to define your bonded 
parameters based on the names present in the coordinate file.  This is an 
incorrect approach.  Refer to existing force fields and the manual for examples.



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


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