Justin<br><br><br>1) So if I understood correctly I can make parametrisation of my uncommon group by the atb for instance. Than I can change itp file to rtp form and integrate this new residue to the existing ff. Finally when I will run pdb2gmx on the protein with the same group (even with different atom order) I obtain proper topology.top file. Doest it correct ?<br>
<br><br>2) I've defined bond between both of my atoms as the gb_15 and define this atoms as the C in the topology.top. Than I've run minimisation and short 3ns MD_run. Unfortunatelly this atoms was in the sp3 form and were not in the planar form :( What else should I do ? Could some operations with the angle term in topology.top help me? I've modified 612 613 614 2 as the ga_27 but it also could not help me.<br>
<br><br><br>James<br><br><div class="gmail_quote">2012/6/10 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
On 6/10/12 8:03 AM, James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Justin,<br>
<br>
thanks again for help.<br>
<br>
Finally is there any generall solution to parametrise hetero-groups covalently<br>
bonded with the protein ? Many proteins consist of such groups e.g chromophore<br>
in GFP, retinall in rhodopsin as well as some prostetic groups in the enzymes.<br>
<br>
</blockquote>
<br></div>
Parameterization schemes differ across force fields. It's never easy.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I've tried to make something like you've told me via inclusion of<br>
pre-parametrised residues in the existing gromacs ff but forced with some<br>
problems due to the atom order in new ITP and gro files provided by ATb or<br>
PRODRG are different from initial pdb file so pdb2gmx on the whole protein where<br>
het-group in the old order would not work properly :(<br>
<br>
</blockquote>
<br></div>
The output .itp files of ATB or PRODRG are not what you should be using. You can't #include a covalently attached residue and expect the resulting dynamics to be relevant; it's not like a ligand.<br>
<br>
What you need to do in those cases is create an .rtp entry (and any other incidental bonded and nonbonded additions, as stated before) that specifies whatever parameters you believe to be reliable. At that point, when the .rtp file is read, the atom order is irrelevant - if pdb2gmx finds the atoms it needs, it builds the topology.<div class="HOEnZb">
<div class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<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>
<br>
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