[gmx-users] Question about "atom" field in .top / .itp file vs ffnonbonded.itp

[Justin Lemkul]

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


-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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