I remember doing Lys bound ligands in the past using the info from the
manuals, but recently I discover that you can do the same using RED server.
Unfortunately the website has been down for the last couple of days, so I
can not link the instructions for preparing the ligand.
2015-10-10 1:14 GMT+02:00 Jim Wu <jwu.g.hmc.edu>:
> 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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>
--
Dr. Emilio Lence Quintana
Organic Chemistry Department-CIQUS
University of Santiago de Compostela
15782 Santiago de Compostela, Spain
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Received on Sat Oct 10 2015 - 04:30:04 PDT
