[AMBER] Making Parameter and Topology Files for Protein-Ligand Complex

From: Jim Wu <jwu.g.hmc.edu>
Date: Fri, 9 Oct 2015 16:14:09 -0700

Hi everyone,

I am currently trying to create parameter and topology file for retinal
with Schiff Base linkage to Lys296 in rhodopsin. I have tried combing
through the AMBER tutorials, however I am having trouble applying the same
methods for my system. Furthermore, some of these tutorials are based on
older versions of AMBER and sometimes use other software that I do not know
how to use yet.

First, I renamed the RET and LYS296 to REL in the rhodopsin pdb file and
then I separated the retinal linked with Lys296 from the .pdb file. Using
Gaussian 09 I used the MK population analysis approach to setup for
Antechamber RESP fitting. Here are my antechamber inputs:

$ antechamber -i retlys.log -fi gout -o retlys.prepin -fo prepi -c resp -s
2 -at gaff
$ antechamber -i retlys.log -fi gout -o retlys.mol2 -fo mol2 -c resp -s 2
-at gaff
$ parmchk2 -i retlys.prepin -fi prepi -o retlys.frcmod

Now I go to xleap to create the .lib file

$ xleap
> source leaprc.ff14SB
> source leaprc.gaff
> loadamberparams retlys.frcmod
> loadamberprep retlys.prepin
> REL = loadmol2 retlys.mol2
> saveoff REL retlys.lib

I know I have to use this retlys.lib file so that we have the values for
all the bonds, angles, and charges, but I do not know how to use this
correctly.

I tried to load the .frcmod and .lib files and the pdb file for rhodopsin
with retinal. However, I am still finding that missing parameters. Looking
closer, I realized that these were exactly the parameters for the retinal
molecule. Furthermore, there were some strange bonds and it did not look
like retinal at all.

Can someone please explain to me the general method for correctly creating
the .prmtop and .inpcrd files for a protein-ligand complex? Am I going
along the right track?

Thanks,
Jim Wu
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Received on Fri Oct 09 2015 - 16:30:03 PDT
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