On Wed, 2014-03-05 at 16:16 +0800, 闫玉娜 wrote:
> Hi al ,
> I have use xleap to produce a small molecular of 'ch3cn',and I want to use
> antechamber to produce the prmtop file. I don't know how to correct it. Can
> you help me to resolve it ? Thank you very much
>
>
> The PDB file:4.pdb
> ATOM 1 C1 LIG 1 -0.000 -0.000 -0.000 1.00 0.00
> ATOM 2 H1 LIG 1 1.000 0.000 0.000 1.00 0.00
> ATOM 3 H2 LIG 1 -0.334 0.943 0.000 1.00 0.00
> ATOM 4 H3 LIG 1 -0.334 -0.472 0.816 1.00 0.00
> ATOM 5 C2 LIG 1 -0.434 -0.614 -1.061 1.00 0.00
> ATOM 6 N1 LIG 1 -0.801 -1.134 -1.958 1.00 0.00
> TER
>
> Command:
> antechamber -i 4.pdb -fi pdb -o 4.mol2 -fo mol2 -j 5 -c bcc
> parmchk -i 4.mol2 -f mol2 -o 4.frcmod
>
> Leapin：
> source leaprc.ff99SB
> LIG = loadmol2 4.mol2
> check LIG
> loadamberparams 4.frcmod
> saveoff LIG 4.lib
> saveamberparm LIG 4.prmtop 4.inpcrd
antechamber automatically applies gaff atom types when it does its atom
type determination. Parmchk then goes through gaff.dat to determine
what any missing parameters might be. By default, parmchk only adds
parameters that cannot be found in gaff.dat so in order to make leap
find all of the parameters you need to load the gaff force field using
the command:
source leaprc.gaff
Alternatively, you can use the "-a Y" flag in parmchk to have it print
out all parameters in the frcmod file (in which case sourcing
leaprc.gaff is unnecessary).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 05 2014 - 05:00:03 PST
