Thanks Justin,<div><br></div><div>I think that I have to write a script to remove hydrogens that are not suitable for united-atom forcefield. After this operation I can use pdb2gmx. <br><br><div class="gmail_quote">On Fri, Oct 29, 2010 at 10:05 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div></div><div class="h5"><br>
<br>
Deniz KARASU wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
<br>
I'm trying to convert a protein, that is protonated with another special software and by manually checking, with pdb2gmx. I am using FF53A6 forcefield and don't use -ignh option. When I run pdb2gmx it gives me this error. <br>
<br>
Atom HA in residue VAL 1 not found in rtp entry with 8 atoms<br>
while sorting atoms. Maybe different protonation state.<br>
Remove this hydrogen or choose a different protonation state.<br>
Option -ignh will ignore all hydrogens in the input.<br>
<br>
I understand that the hydrogen atom is not defined in forcefield for VAL residue and need selection protonation state interactively. <br>
I wonder that there is anyway to convert protonated protein for specified forcefield (including united-atom ff) and assign automatically protonation state according to bonded hydrogen in structure?<br>
<br>
</blockquote>
<br></div></div>
You can't choose to ignore some H atoms while recognizing others. Either you provide pdb2gmx with a suitable structure that can be used exactly by the force field, or you let pdb2gmx assign protonation states after ignoring all input H atoms. Fortunately, for all termini and titratable residues, you can do so with the -ter and -inter options.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks.<br>
<br>
Deniz. <br>
</blockquote>
<br>
-- <br>
========================================<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.vt.edu/Pages/Personal/justin</a><br>
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