exactly<br><br>all hydrogens were represented as a part of the groupd in wich they were. So is there possible way to explicit it?<br><br>Another question about pdb2gmx. about -term<br>as I understood this must be used only if atoms for CAP groups are presented in the PDB file mustnt it?<br>
So what term exactly do? Doest it make a connection beetween CAP and C and N termi or anothing else?<br><br><br>James<br><br><div class="gmail_quote">2011/10/31 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">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>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Its very unclear for me because after pdb2gmx -f 1.pdb -o conf.gro -ignh with gromos force field<br>
<br>
I've checked conf.gro by VMD and this structure didnt contains any hydrogens ;o<br>
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</blockquote>
<br></div>
I highly doubt that. I've used one of the Gromos96 force fields for nearly all of my work and it has never failed in any Gromacs version. Perhaps you're simply not taking into account the fact that Gromos96 parameter sets are united atom, meaning that aliphatic hydrogens are not represented explicitly.<div>
<div></div><div class="h5"><br>
<br>
-Justin<br>
<br>
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Justin A. Lemkul<br>
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Virginia Tech<br>
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