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 - 08:00:04 PST
