[gmx-users] regarding pdb2gmx

Justin Lemkul jalemkul at vt.edu
Sun May 31 14:44:02 CEST 2015

On 5/31/15 8:37 AM, soumadwip ghosh wrote:
> Thank you very much for your help Justin. I really appreciate
> I would like to bother you for one last time ( as of now ;). So, if I
> am dealing with a non-trivial molecule like CNT or some
> polyelectrolyte and I mainly intend to demonstrate the non-bonding
> interactions with some nucleic acids (say a CNT-dsDNA ) interaction,
> it appears to me that I dont need to care about the DNA topology even
> if it lacks the said parameters but I do have to care about these
> while updating the cnt.itp files since grompp complains about the
> missing parameters in the cnt.itp file. If one does not write the [
> atomtypes ] and the [ pairtypes ] sections in the cnt.itp file and
> misses out the sigma and epsilon terms I think it underestimates the
> non-bonding energy terms of interaction between DNA bases and CNT
> atoms in the md.edr file to some extent. I will appreciate your
> opinion on this statement.

That doesn't make sense.  If you are missing parameters, grompp will complain 
and fail with a fatal error.  If grompp happily carries on and produces your 
.tpr, then you're getting the interactions the force field dictates because 
grompp found everything the molecules need in ffbonded.itp, ffnonbonded.itp, or 
specified in a molecule .itp.  If you override grompp's messages with -maxwarn, 
well then that's your fault :)

Also note that [pairtypes] are intramolecular terms.  They do not affect DNA-CNT 



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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