You could use GLYCAM which is in AMBER so the parameters are already there in the correct format (but not in the AMBER ported to GROMACS) and convert that to GROMACS topology. It'll save you some time :)<br>I had problems converting the improper dihedral that holds the NAc group planar using <a href="http://amb2gmx.pl">amb2gmx.pl</a> so keep an eye on it.<br>
<br>Good Luck,<br><br>Oliver<br><br><div class="gmail_quote">On 15 November 2010 22:15, Anthony Cruz Balberdi <span dir="ltr"><<a href="mailto:anthony.cruz5@upr.edu">anthony.cruz5@upr.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Yuvraj:<br>
<br>
There is a protocol to find the charges and force field parameters for<br>
new molecules for the AMBER force field. The best way is to try to<br>
find the parameters from a publication. If you dont find anything then<br>
use RED to find the charges (<a href="http://q4md-forcefieldtools.org/RED/" target="_blank">http://q4md-forcefieldtools.org/RED/</a>).<br>
Then use ambertools to find the necessary force field parameters and<br>
generate an AMBER topology. After that use acpype to transform the<br>
amber topology to a GROMACS topology. From the GROMACS topology the<br>
create an itp file to use in your GROMACS TOPOLOGY.<br>
<br>
To better understand what I said please read the reference for the<br>
force field, the GROMACS manual and the RED tutorial.<br>
<br>
Best Regards,<br>
<br>
Anthony<br>
<div><div></div><div class="h5"><br>
<br>
<br>
On Mon, Nov 15, 2010 at 5:13 PM, YUVRAJ UBOVEJA <<a href="mailto:yuvrajthedon@gmail.com">yuvrajthedon@gmail.com</a>> wrote:<br>
> How to parametrize N-acetyl Glucosamine present in my PDB file with AMBER<br>
> force field to use in GROMACS.<br>
> Please suggest some solutions.<br>
><br>
> Thanks<br>
><br>
> --<br>
> Yuvraj<br>
><br>
><br>
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