Dear Aurum,
If you use R.E.D., provide a P2N input file, describe the atoms
involved in the intra-molecular charge constraints (i.e. you use the
INTRA-MCC keyword), you will automatically generate a central fragment
for your target amino-acid in a single step. At the end you get a FF
library in the mol2 file format.
See tutorials .
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
See examples in R.E.DD.B. as well
http://q4md-forcefieldtools.org/REDDB/Projects/F-1/
& the corresponding RESP inputs:
http://q4md-forcefieldtools.org/REDDB/Projects/F-1/input1.in
http://q4md-forcefieldtools.org/REDDB/Projects/F-1/input2.in
regards, Francois
>> From the manual of AmberTools1.2, I get information of respgen.
> "
> Usage: respgen -i inputfile (ac)
> "
> So, If I want to run respgen, I must prepare the ".ac" file for
> input file. But what's the format of ".ac" and how do generate it?
>
> In additions, I found the antechamber's
> tutorial(http://ambermd.org/antechamber/pro4.html):
> "respgen -i pro4a.mol2 -o pro4-step1.respin -f resp1"
> "respgen -i pro4a.mol2 -o pro4-step2.respin -f resp2"
> This is not produce the correct result for "pro4-step1.respin" by
> using "*.mol2", so it maybe need the ".ac" format file, or the
> tutorial is wrong?
>
> How do I generate the file of "Pro4.crg"?
>
> I could not finish this
> tutorial(http://ambermd.org/antechamber/pro4.html) by Amber10. Could
> you give me an advice as soon as possible?
>
> Thanks
> Aurum
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Received on Fri Feb 05 2010 - 09:30:03 PST
