Thanks for the replys. The problem appeared to be very simple, all I had to
do is to replace "ELECTROSTATIC" with "ELECTRIC" in the GAMESS dat file for
the script to work fine
On 19 August 2015 at 21:48, <cieplak.cgl.ucsf.edu> wrote:
> It seems that this esp.in file is not prepared correctly.
> It has many zero's in place of x,y,z positions for espot points,
> and electrostatic potentials (first column) should be of the order of
> magnitude
> smaller (and non-zeros).
> Something is wrong with extracting properly espots from Gamess outputs.
> You can do that using PyRED program.
>
> Piotr
>
>
>
> August 19 2015 5:47 AM, "Mahmood Jasim" <ddfd09.gmail.com> wrote:
> >
> > esp.in
> > <
> https://drive.google.com/file/d/0B2P4Qp842kSiY0tHZ2JnQzI0NGM/view?usp=drive_web
> >
> > Hi Amber Users
> >
> > I have problems with RESP fitting. I am using GAMESS to generate the
> > electrostatic grid for my ligand and I am using the "Run.resp" script
> > (attached) to generate the input files for RESP (resp.in and esp.in
> > attached). I then run RESP using:
> >
> > resp -i resp.in -o resp.out -e esp.in
> >
> > I do get the out file (resp.out attached) but the charges are so extreme
> > ranging from -21 to 21 although the electrostatic grid has been generated
> > by an optimisation calculation in GAMESS. Also when I use a programme
> > called Molby to assign the charges, the latter gives mereasonable values
> > for the charges.
> >
> > I cannot use Molby because I have a cap attached to my molecule composed
> of
> > the final 5 atoms. I modified the resp.in file (resp_cap.in attached) to
> > fix the charges of the cap according to their values in the Amber
> > forcefield and created a file for the fixed charges of the cap (SCH3_cap
> > attached) and ran RESP as:
> >
> > resp -i resp_cap.in -o resp_cap.out -e esp.in -q SCH3_cap.qin
> >
> > The file shows this "not enough (possibly none) q0 are given in file
> > ESP.Q0, so the remaining old ones will be used." and the charges of the
> cap
> > atoms are fixed to zero.
> >
> > Could anyone please help me with this?
> >
> > Best Regards,
> > Mahmood Jasim
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Aug 20 2015 - 09:00:03 PDT
