Re: AMBER: XLeap: head/tail and frcmod

From: David A. Case <>
Date: Mon, 12 Apr 2004 08:15:29 -0700

On Mon, Apr 12, 2004, L Jin wrote:
> I have a question about xleap. we can set head/tail atoms for the unit. What if
> one unit does not have a head/tail atom? It seems that this head/tail missing
> unit just could not be sequenced/combined with other normal units. Will this
> lack affect other parameters or calculations with sander?

As you point out, a unit does not need a HEAD and TAIL unless you intend
to include it into the middle of a polymers sequence with covalent bonds.
> Another quesiton about loading parameters.S-P.dat is a frcmod I used to modify
> the force field. When I loaded it together with parm99 leap gave me the
> following message:
> Loading parameters: /usr/progs/amber/dat/leap/parm/S-P.dat
> Reading force field mod type file (frcmod)
> Unknown keyword: SO 32. in parameter file.

Looks you you are missing the title card or the MASS keyword in your frcmod
file. There are a number of examples of frcmod files in the
$AMBERHOME/test/antechamber directories; comare you file to those. If that
doesn't help, you will have to post your frcmod file.

....good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Mon Apr 12 2004 - 16:53:00 PDT
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