Hi!
Does the all oxygen atoms connected have near about -1 charge? If so It
might be due to high repulsion between negative oxygen atoms and small
attraction to positive sulfur.
I faced similar issue with ATP. Issue got resolved when I added
co-ordinated MG ion to these oxygen atoms. You can even add hydrogen atoms
to the oxygen atoms if you are ok with it.
It might be some other issue as well. Check the co-ordinates of minimized
structure if the structure is distorted then minimization also did not go
that well.
I hope it helps.
Regards
Abhilash
On Thu, Feb 2, 2017 at 9:23 AM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> When your minimization was completed did you check the forces on your
> system??
> Check the "GMAX" and the corresponding atom.
>
> 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: Balaji Selvam [mailto:bselvam01.gmail.com]
> Sent: Thursday, February 02, 2017 12:03 AM
> To: amber.ambermd.org
> Subject: [AMBER] Thiophosphate paramters - AMBER
>
> Dear Amber Users,
>
> I am trying to simulate a MD system where the protein bound to
> guanosine-diphosphate-monothiophostate (GSP).
>
> I generated the GSP parameters using GAFF and build the system with tleap.
>
> The minimization procedure ran without any error.
>
> The problem occurs when I moved the system to MD runs.
>
> The writing the files for every steps shows that phosphate and sulphur
> group overlap each other and the simulation crashes.
>
> Could you please advice to get parameters for thiophosphate group
>
> Thank You,
> Balaji
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Received on Thu Feb 02 2017 - 06:00:03 PST
