That would mean that a new residue type will not be required? I just need the correct input D-coordinates? <br><br><div class="gmail_quote">On Sat, Mar 26, 2011 at 2:02 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 26/03/2011 2:27 AM, maria goranovic wrote:
<blockquote type="cite">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 ?</blockquote>
<br></div>
Unlike (say) AMBER's leap, pdb2gmx doesn't generate coordinates in a
general sense. It generates a topology that matches given
coordinates, fixing a few details as directed. It will fill valences
with hydrogen atoms, generate terminal groups, organize disulfides,
and choose protonation states of titratable residues, but it won't
change geometries in the way you seem to want.<br>
<br>
Neither does anything in the .top/.itp files stipulate the chirality
of any center (in all-atom models). Various dihedral angles change
sign with chirality, but the dihedral functions are all symmetric
about the y-axis (i.e. even). So I suspect you do not need to change
anything about the topology. Just use a molecule builder to change
the chirality of the relevant center in the input file to pdb2gmx.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">
<div>
<div>
<div class="gmail_quote">On Fri, Mar 25, 2011 at 12:24 PM,
Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);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><<a href="mailto:mariagoranovic@gmail.com" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">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>
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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>
>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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before posting!<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" target="_blank">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>
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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>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><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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</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
</div>
</div>
</blockquote>
<br>
</div></div></div>
<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 <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>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>
Copenhagen<br>