Thanks for your explanation!
As the frcmod file described as "the same as hn-n etc.", and the parameters generated by the parmchk is dependent on the gaff force field instead of any amber force fields. Is my comprehension right? I need your answer.
Best,
Jinfeng
At 2014-05-12 22:56:35,"Jason Swails" <jason.swails.gmail.com> wrote:
>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 Tue May 13 2014 - 03:30:02 PDT
