On Mon, 2014-05-12 at 22:24 +0800, Jinfeng Huang wrote:
> Thanks for your helps! I tried the command as you provided , and I have another confusion about the " parmchk " . I used the following commands , and I got the same two frcmod files.
> -------------------------------------------------------------Commands-----------------------------------------------------
> parmchk -i *.prep -f prepi -o blah.frcmod -p $AMBERHOME/dat/leap/parm/gaff.dat
> parmchk -i *.prep -f prepi -o blah.frcmod
These two commands are equivalent. gaff.dat is the default parameter
database that parmchk uses. If you want to use one of the Amber
parameter sets, you should use the command:
parmchk -i *.prep -f prepi -o blah.frcmod -p $AMBERHOME/dat/leap/parm/parm10.dat
> -----------------------------------------------------------------------------------------------------------------------------------
> --------------------------------------------------------Part of the frcmod file--------------------------------------------
>
> BOND
> N -H 410.20 1.009 same as hn-n
> N -CT 330.60 1.460 same as c3-n
> CT-CT 303.10 1.535 same as c3-c3
> CT-H1 337.30 1.092 same as c3-hc
> CT-HC 337.30 1.092 same as c3-hc
> CT-OH 314.10 1.426 same as c3-oh
parmchk is using the gaff parameters, and apparently has some type of
mapping from amber atom types to gaff atom types. See the "same as ..."
comments that show which gaff parameter types were assigned to that
parameter.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon May 12 2014 - 08:00:02 PDT
