Justin, hello!<br><br><br>I've found that D and L-isomers must be topological identicaly so I've used topology of Leu and Val residues for Dle and Dva resp.<br><br>I've added information about topology of that two residues to the <a title="Documentation/File Formats/.rtp File" rel="internal" href="http://www.gromacs.org/Documentation/File_Formats/.rtp_File">.rtp .hdb of my force field as well as to the </a><a title="Documentation/File Formats/residuetypes.dat" rel="internal" href="http://www.gromacs.org/Documentation/File_Formats/residuetypes.dat">residuetypes.dat</a> <br>
<br>Then I've succsesfull generated topology for gramicidin via pdb2gmx.<br><br>I have only questions about two terminal CAP groups used in the Gramicidin<br><br>It was FOR group on the C-end <br><br>HETATM 1 C FOR A 1A -3.690 -1.575 -2.801 1.00 0.00 C <br>
HETATM 2 O FOR A 1A -3.774 -1.363 -1.586 1.00 0.00 O <br>HETATM 3 H FOR A 1A -4.305 -1.047 -3.545 1.00 0.00 H <br><br>and the ETA group on the N-end<br><br>HETATM 267 C1 ETA A 15A 5.148 -0.421 8.762 1.00 0.00 C <br>
HETATM 268 C2 ETA A 15A 3.657 -0.080 8.832 1.00 0.00 C <br>HETATM 269 N ETA A 15A 2.813 -1.244 8.933 1.00 0.00 N <br>HETATM 270 O ETA A 15A 5.921 0.752 8.985 1.00 0.00 O <br>
HETATM 271 1HN ETA A 15A 2.507 -1.491 9.845 1.00 0.00 H <br>HETATM 272 HO ETA A 15A 5.736 1.339 8.244 1.00 0.00 H <br>HETATM 273 1H1 ETA A 15A 5.410 -1.174 9.531 1.00 0.00 H <br>
HETATM 274 2H1 ETA A 15A 5.374 -0.849 7.759 1.00 0.00 H <br>HETATM 275 1H2 ETA A 15A 3.383 0.525 7.938 1.00 0.00 H <br>HETATM 276 2H2 ETA A 15A 3.492 0.565 9.718 1.00 0.00 <br>
<br>I could not find good analogue for that groups in Amber force field so I've desided to deleate that groups temporary.<br>Could you tell me how I can add possible Caps on the C and N terms of each chain of my molecule via pdb2gmx ? <br>
In one tutorial I've found the -term function for that but in my case system didnt suggest me to add new caps<br><br><br><br>James<br><br><div class="gmail_quote">2011/10/28 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Gromacs users!<br>
<br>
I've forced with some problem of preparing topology of my input pdb via pdb2gmx.<br>
<br>
My input structure( gramicidin ion chanell) consist of some heteroatoms due to the presence of the non standart aminoacids in sequence: FOR, DLE, DVA, ETA ( this the R isomers instad of L analogs)<br>
<br>
<br>
I've tried to parametriesed that structure via different force fields but in all cases there are not suitable topologies for that aminoacids<br>
<br>
e.g<br>
Fatal error:<br>
Residue 'FOR' not found in residue topology database<br>
<br>
How I can solve that problem? I've tried to look for the suitable itp file but could not find it too :(<br>
</blockquote>
<br></div></div>
For new protein residues, you do not need an .itp file, you need a suitable .rtp entry such that pdb2gmx can incorporate it into your topology.<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/<u></u>Parameterization</a><br>
<a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/Adding_<u></u>a_Residue_to_a_Force_Field</a><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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