I do recommend amber ff99sb, but have a read in some papers that is referred in acpype website. Also, getting the mdp file tuned will require testing. The mdp you see in acpype website are examples that work but surely need tweaking for production and for that I recommend you to read gmx manual carefully.<div>
<br></div><div>Then you can come with more specific questions.</div><div><br></div><div>Alan<br><br><div class="gmail_quote">On 21 September 2010 08:03, vivek sharma <span dir="ltr"><<a href="mailto:viveksharma.iitb@gmail.com">viveksharma.iitb@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi,<br>
Thanks Manoj and Alan for your quick response. I am already using the<br>
ambertools to generate the topology and these topologies are<br>
successfully accepted in gromacs. I will have a look at alternate<br>
methodologies and workflow that you guys have suggested.<br>
<br>
My question is can I have any idea that which version of AMBER FF<br>
should be used in this case of drug-enzyme complex?<br>
Also, can I have any idea about the selection of MD parameters, (which<br>
goes in mdp file) that should be used in this case?<br>
<br>
With thanks,<br>
<font color="#888888">Vivek<br>
</font><div><div></div><div class="h5"><br>
On 21 September 2010 12:24, Alan <<a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a>> wrote:<br>
> Also, have a read at <a href="http://acpype.googlecode.com" target="_blank">acpype.googlecode.com</a>.<br>
> Alan<br>
><br>
> On 21 September 2010 06:36, manoj singh <<a href="mailto:mks.amber@gmail.com">mks.amber@gmail.com</a>> wrote:<br>
>><br>
>> First, you have to develop parameter for your molecule withing Amber. Then<br>
>> you have to create .prmtop and .inpcrd files for your molecule, and than you<br>
>> can convert the Amber topology to Gromacs topology. You will need AmberTools<br>
>> and a script called <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a>.<br>
>><br>
>> Following links would be helpful for you<br>
>><br>
>> <a href="http://ambermd.org/#AmberTools" target="_blank">http://ambermd.org/#AmberTools</a><br>
>><br>
>> <a href="http://ambermd.org/antechamber/efz.html" target="_blank">http://ambermd.org/antechamber/efz.html</a><br>
>><br>
>> <a href="http://ffamber.cnsm.csulb.edu/amb2gmx.pl" target="_blank">ffamber.cnsm.csulb.edu/amb2gmx.pl</a><br>
>><br>
>> On Tue, Sep 21, 2010 at 12:51 AM, vivek sharma<br>
>> <<a href="mailto:viveksharma.iitb@gmail.com">viveksharma.iitb@gmail.com</a>> wrote:<br>
>>><br>
>>> Hi There,<br>
>>> I am trying to run molecular dynamics on a drug-enzyme complex using<br>
>>> amber force field. I have done it earlier using gromos FF using<br>
>>> drug-enzyme tutorial, I dont know if the parameter set (.mdp file)<br>
>>> will be same or different while using AMBER FF.<br>
>>> Any insight/comments into the matter may be of help if somebody has<br>
>>> tried using AMBER FF for docked complex in GROMACS.<br>
>>><br>
>>> Thanks in advance.<br>
>>><br>
>>> regards,<br>
>>> Vivek<br>
>>> --<br>
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>><br>
>><br>
>> --<br>
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>> Please don't post (un)subscribe requests to the list. Use the<br>
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><br>
><br>
><br>
> --<br>
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>
> Department of Biochemistry, University of Cambridge.<br>
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>>><a href="http://www.bio.cam.ac.uk/~awd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
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><br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div>