Thanks for the reply.
I have used RESP charges but the result is same.
One time I somehow managed to run the equillibartion step but at around
100000 step ,the system blown up and the bond between P and O got
elongated enormously.
On Sun, Mar 5, 2017 at 10:58 AM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> Thanks for the details
> Try to use RESP method to fit the partial charges (derived using pop=mk in
> Gaussian using amber compatible iops)
> And in antechamber use the flags -nc -1 (since your's in monoanionic) -at
> gaff -c resp in addition to what you must have used.
>
>
> Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in
> Skype. adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: Mrinal Arandhara [mailto:arandharamrinal.gmail.com]
> Sent: Sunday, March 05, 2017 9:24 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] dUMP parameters
>
> I derived charges by using gaussian (esp) . I have also tried the AM1-BCC
> charges.
>
> On Sun, Mar 5, 2017 at 10:37 AM, Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
> > Sorry,
> > I meant How did you derive the partial charges?
> >
> > Best Regards
> >
> >
> >
> > Elvis Martis
> > Ph.D. Student (Computational Chemistry) at Bombay College of Pharmacy
> >
> >
> > A Kalina, Santacruz [E], Mumbai 400098, INDIA
> > W www.elvismartis.in
> > Skype. adrian_elvis12
> >
> >
> >
> >
> > -----Original Message-----
> > From: Mrinal Arandhara [mailto:arandharamrinal.gmail.com]
> > Sent: Sunday, March 05, 2017 8:51 PM
> > To: amber.ambermd.org
> > Subject: [AMBER] dUMP parameters
> >
> > I'm trying to run a MD simulation of protien-ligand complex with
> > dUMP(monoanionic) as cofactor. The gaff parameters for dUMP generated
> by
> > parmchk has reasonable penalty values but after minimisation step two
> > atoms(one O and the other hydroxyl-H) attached to the P-atom are
> sitting
> > on top of each other and 1-4 EEL value is very large (*************) .Is
> > it due to wrong force field parameters or wrong charges ??Are the
> > parameters for dUMP available ??
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Received on Sun Mar 05 2017 - 08:30:02 PST
