Re: [AMBER] Thiophosphate paramters - AMBER

From: Elvis Martis <>
Date: Thu, 2 Feb 2017 03:53:02 +0000

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
Skype. adrian_elvis12

-----Original Message-----
From: Balaji Selvam []
Sent: Thursday, February 02, 2017 12:03 AM
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,
AMBER mailing list

AMBER mailing list
Received on Wed Feb 01 2017 - 20:00:02 PST
Custom Search