Hi,<br><br>Not sure exactly what you plan to simulate but here are a couple of potential pitfalls:<br><br>Does acpype call <a href="http://amb2gmx.pl">amb2gmx.pl</a> or is it new code that converts? If it is a <a href="http://amb2gmx.pl">amb2gmx.pl</a> call I'd check the torsions on the NAc group if you have one. They didn't get translated when I used it.<br>
<br>When using amber ports be careful about using default index groups like "protein" or "C alpha" as they won't contain atoms from residues like LYP that are different in the ports.<br><br>Also you'll want to set fudge to 1.0 in the amber99sb.itp or where it is set (can't check this atm) if simulating the sugar alone. Its due to differences in the way amber and glycam are parametrized. (If you are interested it is differences in 1-4 scaling).<br>
<br>There may be other issues I'm not aware of yet. :)<br><br>All the best,<br>Oliver<br><br><div class="gmail_quote">On 23 December 2010 18:13, Alan Wilter Sousa da Silva <span dir="ltr"><<a href="mailto:awilter@ebi.ac.uk">awilter@ebi.ac.uk</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;">Have a look at <a href="http://acpype.googlecode.com" target="_blank">acpype.googlecode.com</a><div>
<br></div><div>Alan<br><br><div class="gmail_quote">2010/12/23 gromacs564 <span dir="ltr"><<a href="mailto:gromacs564@126.com" target="_blank">gromacs564@126.com</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5"><div><span style="text-transform: none; text-indent: 0px; border-collapse: separate; font: medium Simsun; white-space: normal; letter-spacing: normal; color: rgb(0, 0, 0); word-spacing: 0px;"><pre>
Hi ,
I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam web(they are glycam06 force field,included in AMBER) ,<span> </span> but cannot converted this amber files to gromacs files format.</pre><pre>
Can anyone help me to convert this (amber) files to gromacs input files(top or itp,gro).?
Many thanks!</pre></span><br></div>
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