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: case.scripps.edu
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 | http://www.scripps.edu/case
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Received on Mon Apr 12 2004 - 16:53:00 PDT
