[gmx-users] Fwd: Gromacs_trouble

[Mark Abraham]

Hi,

Please keep discussions on the mailing list. I have no experience of 
Martini, and don't have the ability to give my time for individual help. 
I would advise you to simplify your system as much as you can. Get a 
stable simulation of a single glutamate residue working, then change to 
a singly-carboxylated residue, and slowly work up. Now when things go 
wrong you can work out what is wrong.

Mark

-------- Original Message --------
Subject: 	Gromacs_trouble
Date: 	Wed, 14 Sep 2011 17:19:01 +0200
From: 	Du Jiangfeng (BIOCH) <j.du at maastrichtuniversity.nl>
To: 	Mark.Abraham at anu.edu.au <mark.abraham at anu.edu.au>



Hi Mark,

Thanks for your attention.

In fact, i appended the carboxylated Glutamate values into martini force field, and I got my protein model. However, no matter how to perform EM, the MD simulation was brown up because of too many links warns.

I presume the problem is still in the values of the modified residues in the itp file. Could you help me more? If you don't mind, I would like to attach the method of how I did it.

Thank you in advance,

Best Wishes,

Jiang.





On 8/09/2011 6:29 PM, Du Jiangfeng (BIOCH) wrote:
>  Dear Everyone,
>
>  I am going to simulate the interaction of prothrombin's Gla domain with membrane in martini force field. Here I encountered a problem: there are 10 modified GLUs in GLA domain. Martini force field can't recognize them. How should I overcome this problem?
>
>  What I want to do now is to add this modified residue into martini force field, but I do not know whether it is feasible or logical? What's worse, I really don't know what is BNLN, BNKB or ANGL? Where can I get some references about this story?

Depending on the details of the modified GLU, you will need to consider
the points made at
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field,
http://www.gromacs.org/Documentation/How-tos/Parameterization and in the
Martini documentation.

Mark


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