[gmx-users] Question about "atom" field in .top / .itp file vs ffnonbonded.itp
jalemkul at vt.edu
Thu Jul 10 00:01:42 CEST 2014
On 7/9/14, 5:08 PM, Eric Smoll wrote:
> Hello Gromacs Users,
> Can the atom field (e.g., "H") of a .top / .itp file differ from the atom
> field of the .gro file and, for instance, the ffnonbonded.itp file? What
> are the restrictions here?
> My guess is that the .top /.itp will reference with the ffnonbonded.itp
> with the type field only (e.g., opls_900). But can the atom tags differ
> between these two files ("HA" vs "H", for instance). Can both atom tags
> differ from the tags in the .gro file?
The second column of ffnonbonded.itp has nothing to do (directly) with system
topologies or coordinate files. It is a bonded atom type (hence the column
title "bond_type"), which is a translated type used in ffbonded.itp. Since
there are far fewer bond types than there are nonbonded types, this keeps the
files compact by avoiding unnecessary redundancy in ffbonded.itp.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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