Thanks! for reply
>> But it's a good idea to check for yourself, using (say) the rdparm program.
Sure I will check them. top2ff can also be used.
________________________________
From: David A Case <case.biomaps.rutgers.edu>
To: Jio M <jiomm.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, June 27, 2012 5:35 PM
Subject: Re: [AMBER] gaff.dat column and preference to frcmod file params
On Wed, Jun 27, 2012, Jio M wrote:
>
> I have some query about gaff.dat file and in general:
>
> 1) e.g. in gaff.dat for bond, input is:
> c -c 290.1 1.550 SOURCE1 31 0.0080 0.0100
>
> I have checked in http://ambermd.org/formats.html#parm.dat, but not able
> to get what does fourth (source1) to seventh (0.0100) column means and
> some links from scrips.edu (suggested in archive) are not working
Those columns are comments. Any links to scripps.edu are more than four years
old, and are outdated.
>
> 2) I have some frcmod file saved by some senior fellows which has atom
> type similar to that in parm99.dat.
>
> e.g. (part of frcmod file)
>
> MASS
> CT 12.010 0.878
> HC 1.008 0.135
>
>
> BOND
>
> CT-HC 337.30 1.092
> and I want to use it with parm99.dat (which also uses capital name),
> how I can make leap understand to use those values defined in frcmod
> file without modifying parm99.dat file, as in above case CT-HC is also
> defined in parm99.dat but with different parameter.
The most recently loaded parameters are the ones that get used. So, if you
load the frcmod file after the parm99.dat file, the values in the frcmod file
will be the ones that show up in the prmtop file. But it's a good idea to
check for yourself, using (say) the rdparm program.
....dac
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Received on Wed Jun 27 2012 - 05:30:03 PDT
