Hello
Are you sure that the parameters are already available? In other words did you read the literature and see if somebody has already simulated the same molecule. If not you could try to compute the RESP charges yourself with the RED webserver :
http://upjv.q4md-forcefieldtools.org/REDServer-Development/
Good luck
--------------------------------------------------------------------
Stéphane Abel, Ph.D.
CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 9198
Institut de Biologie Intégrative de la Cellule (I2BC)
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
________________________________________
De : Mrinal Arandhara [arandharamrinal.gmail.com]
Envoyé : dimanche 5 mars 2017 17:06
À : AMBER Mailing List
Objet : Re: [AMBER] dUMP parameters
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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> >
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> >
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Received on Sun Mar 05 2017 - 09:30:02 PST
