The sustiva tutorial is the place to start if you want to create an Amber
library file for your residue. Once you've got that, if the vagaries of
Antechamber's RESP are not to your liking, you can look through the mdgx
charge fitting tutorials:
http://ambermd.org/tutorials/advanced/tutorial28/index.php
The IPolQ charge generation scheme is very involved and still laborious,
but a lot of this owes to what I think of as a converged solution to the
charge set (needs dozens of conformations, plus iterations on top of
that). If all you want is to get a solution to the monopole distribution
that optimizes the electrostatics according to a target QM method like HF /
6-31G*, this would be really easy to do with mdgx once you have the library
files and prmtops.
If you like one conformation in particular, you can use Gaussian to run the
QM and generate cubegen-format files that mdgx will read to give you the
electrostatics, or I could even show you how to bypass most of the IPolQ
procedure and use ORCA to generate the cubegen-format file. Bottom line,
if you want something a little more hands-on, and you have Gaussian or ORCA
available, mdgx can give you fitted charges and an analysis of the
electrostatics versus QM. You can play with things like the extent of
space around the molecule to use in fitting charges, and see how the
results change if you include new conformations.
Dave
On Mon, Jul 1, 2019 at 12:37 PM Sadaf Rani <sadafrani6.gmail.com> wrote:
> thank you Martis
> I have tried it earlier but during the course of this process one of proton
> shifts to another atom when I observe sqm.pdb. As antechamber uses gas
> phase calculation method.
> That is why I am calculating charges by RESP method.
> Any further suggestion please let me know.
> thank you
>
> Sadaf
>
>
> On Mon, Jul 1, 2019 at 4:25 PM Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
>
> > Hello
> > You are looking at an advanced tutorial.
> > Please have a look at this one
> > http://ambermd.org/tutorials/basic/tutorial4b/index.html
> > I guess this is best suited for you.
> >
> > On Monday, July 1, 2019, Sadaf Rani <sadafrani6.gmail.com> wrote:
> >
> > > thank you Martis
> > > but what about RESP fitting as mentioend in this tutorial:
> > > http://ambermd.org/tutorials/advanced/tutorial1/section1.htm
> > >
> > >
> > > Looking forward to hear from you soon
> > >
> > > thank you
> > >
> > > Sadaf
> > >
> > > On Mon, Jul 1, 2019 at 12:21 PM Elvis Martis <elvis.martis.bcp.edu.in>
> > > wrote:
> > >
> > > > Next you must do this
> > > > parmchk2 -i bg6.in -f prepi -o bg6.frcmod
> > > >
> > > >
> > > > Best Regards
> > > >
> > > > Elvis Martis
> > > >
> > > >
> > > >
> > > > ________________________________
> > > > From: Sadaf Rani <sadafrani6.gmail.com>
> > > > Sent: 01 July 2019 16:09
> > > > To: AMBER Mailing List
> > > > Subject: [AMBER] RESP charge calculation
> > > >
> > > > Dear Amber users
> > > > I am trying to calculate RESP charges for my ligand by method as
> > > mentioned
> > > > in following link:-
> > > > http://signe.teokem.lu.se/~ulf/Methods/resp.html
> > > >
> > > > when I am using this command
> > > > antechamber -fi gout -fo prepi -c resp -i BG6.out -o bg6.in -rn BG6
> > > -pf y
> > > > (BG6 is the ligand here)
> > > > I get following files:
> > > > bg6.in, esout, qout and QOUT
> > > > what to do further is not very clear
> > > > Can any body suggest me?
> > > > thank you
> > > > Sadaf
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > Best Regards
> > Elvis Martis
> > Mumbai.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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Received on Mon Jul 01 2019 - 10:00:03 PDT
