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
-----------------------------------------------------------------------------------------------------------------------------------
--------------------------------------------------------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
----------------------------------------------------------------------------------------------------------------------------------
As you you can see above, the atom type are capital letters, but the gaff force field can only recognize the small letters. How can these parameters generated? What is the force field used by the parmchk?
Best wishes!
Jinfeng
At 2014-05-12 19:32:58,"Jason Swails" <jason.swails.gmail.com> wrote:
>On Mon, 2014-05-12 at 17:22 +0800, Jinfeng Huang wrote:
>> Dear amber users,
>>
>> I use the AmberTools 1.5 to generate the parameters of a
>> non-standard amino acid residue , but I don't know what force field I
>> used. What I did are as follows. Firstly, I use the "
>> antechamber ...... -at amber " command to create a prep file. Then I
>> use the "parmchk -i *.prep -f prepi -o *.frcmod " command to receive a
>> frcmod file.
>
>In my experience, if you want to use Amber atom types in antechamber
>then you need to specify a ff parm file for parmchk (because by default
>I believe it looks in the gaff parameter database).
>
>So your parmchk command should have looked something like this:
>
>parmchk -i *.prep -f prepi -o blah.frcmod -p $AMBERHOME/dat/leap/parm/parm10.dat
>
>In this case, you used the parm10.dat parameter database to fill in
>missing parameters. If you then use the commands:
>
>loadAmberParams blah.frcmod
>source leaprc.ff12SB
>...
>
>
>then you are using the ff12SB force field with unknown parameters taken
>from ff10 (which is very similar to ff12SB except for a few sidechain
>torsions, I think, and more importantly it is the main database that
>ff12SB is based on). I would encourage you to compare the atom types of
>your modified amino acid (assigned by antechamber) to the atom types of
>the other standard amino acids to make sure the typing seems reasonable.
>The Amber atom type database for antechamber has not really been changed
>in a long time [1], despite the fact that the standard list of Amber
>atom types has changed quite a bit since then.
>
>Hope this helps,
>Jason
>
>[1] It's been at least 9 years, I think...
>
>--
>Jason M. Swails
>BioMaPS,
>Rutgers University
>Postdoctoral Researcher
>
>
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Received on Mon May 12 2014 - 07:30:05 PDT
