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 - 05:00:02 PDT
