Hi <div><br></div><div>Appreciate the quick help</div><div><br></div><div>I am sorry, this is not an improper, but a proper dihedral that holds the chirality in place. Then the solution suggested by Meli would not work? I do not have a D-ASP. I in fact have an L-ASP which i want to convert to D. So the question is simply how to set the proper chirality to a D-amino acid in CHARMM.</div>
<div><br></div><div><br></div><div><br></div><div>Maria</div><div><br><div class="gmail_quote">On Fri, Mar 25, 2011 at 11:49 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi Maria,<br>
<br>
The CHARMM force field is an all-atom one. That means it does not<br>
require improper dihedrals to maintain chirality. If you have a D-ASP<br>
in your structure file, you can rename it to ASP and just run pdb2gmx.<br>
Mind not to regenerate hydrogens in that case, or make sure to modify<br>
the hydrogen position for the D amino acids afterwards, to set the<br>
proper chirality.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<div><div></div><div class="h5"><br>
On Fri, Mar 25, 2011 at 11:09 AM, maria goranovic<br>
<<a href="mailto:mariagoranovic@gmail.com">mariagoranovic@gmail.com</a>> wrote:<br>
> Hello List<br>
> I want to change an ASP to a D-ASP. I think it should be possible by simply<br>
> changing 2 improper values around the chiral carbon to their opposite sign.<br>
> Instead of making a brand new residue, I thought I would take the topology<br>
> of an ASP generated by pdb2gmx, and simply change values manually in the<br>
> resulting .itp. However, this is not possible because gromacs wants to read<br>
> the dihedral parameters from the ffbonded.itp file. Is it possible for me to<br>
> explicitly state the parameters for these two dihedrals in my d-asp.itp<br>
> file? This will be the fastest solution to the problem because it precludes<br>
> making a new residue or defining new atoms types and so on. With the CHARMM<br>
> force field, I am not sure how q0 cq translate to c0 c1 c2 and c3 which we<br>
> are used to for gromos topologies.<br>
> The mailing list search function was down, so I could not explore prior<br>
> messages about this.<br>
> --<br>
> Maria<br>
><br>
> --<br>
> Maria G.<br>
> Technical University of Denmark<br>
> Copenhagen<br>
><br>
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><br>
<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
<font color="#888888">--<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>
</div>