On 9/18/16 12:30 PM, Sameer Edirisinghe wrote:
Dear users,
There is one thing i cannot clarify from gromacs manual which is about
following error occurred while running grompp

Fatal error:
Unknown bond_atomtype CAY

 I used to create .rtp file from atom types which are already defined in
 atomtype.atp file. But still above error occurring while running grompp.
Not sure should i add again thes atoms to atp file and if so how to add
them. Part of my rtp file is as below, I have modified the ffbonded.itp
(only bond types added) successfully.


What did you add to ffbonded.itp? Whatever it was is causing an error. Based on the .rtp entry below, it looks like you tried to use atom names in ffbonded.itp. That's not right. All interactions (bonded and nonbonded) are defined by atom type. The name is irrelevant. If you're re-using only OPLS-AA atom types, most of the bonded interactions should be present already.

[ bondedtypes ]
; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
  1      1       3          1


You're missing entries here if you're trying to create an OPLS-derived force field. Look at oplsaa.ff/aminoacids.rtp

; MDI
[ MD ]
 [ atoms ]
CAY opls_135  0.000  1
CAX opls_135  0.048 2
CAW opls_135  0.047 2
CAV opls_135  0.144 2
OAU opls_154 -0.112 2


This can't possibly be right. You've defined only heavy atoms (OPLS-AA is an all-atom force field, so there should be H) and the net charge of this residue is +0.117, which is physical nonsense. Based on the names and suspect charges, it looks like you're just porting over a PRODRG united-atom topology and trying to call it OPLS-AA. That's not going to work.

Note that you also need [bonds] if you want the residue to actually be chemically reasonable, otherwise it's just a collection of atoms sitting near one another, which will immediately explode if you try to run a simulation.

-Justin

--
==================================================

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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