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Hi,<br>
<br>
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.<br>
<br>
Mark<br>
<br>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Subject: </th>
<td>Gromacs_trouble</td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Date: </th>
<td>Wed, 14 Sep 2011 17:19:01 +0200</td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">From: </th>
<td>Du Jiangfeng (BIOCH) <a class="moz-txt-link-rfc2396E" href="mailto:j.du@maastrichtuniversity.nl"><j.du@maastrichtuniversity.nl></a></td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">To: </th>
<td><a class="moz-txt-link-abbreviated" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a> <a class="moz-txt-link-rfc2396E" href="mailto:mark.abraham@anu.edu.au"><mark.abraham@anu.edu.au></a></td>
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<pre>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
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a>,
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/How-tos/Parameterization">http://www.gromacs.org/Documentation/How-tos/Parameterization</a> and in the
Martini documentation.
Mark
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