Dear Amber and Dave
I did optimisation in gaussian in solvent for ligand and calculated ESP as
mentioned:
http://ambermd.org/tutorials/advanced/tutorial1/section1.htm
now I use
resp -O -i resp.in -o resp.out -p punch -q qin -t qout
it dont work it gives following error:-
Unit 10 Error on OPEN: espot
what wrong I am putting here?
Please suggest
thank you
Sadaf
On Mon, Jul 1, 2019 at 5:57 PM David Cerutti <dscerutti.gmail.com> wrote:
> 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
> > > > > _______________________________________________
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> > > >
> > >
> > >
> > > --
> > > Best Regards
> > > Elvis Martis
> > > Mumbai.
> > > _______________________________________________
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Received on Mon Jul 01 2019 - 13:00:02 PDT
