Yes, that would be the correct way to do this. I was hoping to take a shorter route, and just modifying a couple of dihedrals in the topology files output by pdb2gmx without having to make a new residue. Is that not possible at all ?<div>
<br></div><div><br><div><br><div class="gmail_quote">On Fri, Mar 25, 2011 at 12:24 PM, 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 general solution is to copy the entry in the .rtp file, modify the<br>
dihedrals involved, and rename the entry to match the name used in the<br>
coordinate (pdb) file. You may also need to copy the entries in the<br>
.hdb file, as well as the .tdb files if it is a terminal residue.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<br>
On Fri, Mar 25, 2011 at 12:12 PM, maria goranovic<br>
<div><div></div><div class="h5"><<a href="mailto:mariagoranovic@gmail.com">mariagoranovic@gmail.com</a>> wrote:<br>
> Hi<br>
> Appreciate the quick help<br>
> I am sorry, this is not an improper, but a proper dihedral that holds the<br>
> chirality in place. Then the solution suggested by Meli would not work? I do<br>
> not have a D-ASP. I in fact have an L-ASP which i want to convert to D. So<br>
> the question is simply how to set the proper chirality to a D-amino acid in<br>
> CHARMM.<br>
><br>
><br>
> Maria<br>
> On Fri, Mar 25, 2011 at 11:49 AM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
> wrote:<br>
>><br>
>> 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>
>><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<br>
>> > simply<br>
>> > changing 2 improper values around the chiral carbon to their opposite<br>
>> > sign.<br>
>> > Instead of making a brand new residue, I thought I would take the<br>
>> > 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<br>
>> > read<br>
>> > the dihedral parameters from the ffbonded.itp file. Is it possible for<br>
>> > 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<br>
>> > precludes<br>
>> > making a new residue or defining new atoms types and so on. With the<br>
>> > CHARMM<br>
>> > force field, I am not sure how q0 cq translate to c0 c1 c2 and c3 which<br>
>> > 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>
>> > --<br>
>> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><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>
>> --<br>
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><br>
><br>
><br>
> --<br>
> Maria G.<br>
> Technical University of Denmark<br>
> Copenhagen<br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<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>
--<br>
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Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
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Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>
</div></div>