If it necessary to manually create force field parameters for each molecule, then how can one run a simulation involving a number of arbitrary molecules (e.g. a set of mono and disaccharides) for which there are no existing force fields?<br>
<br>Do you know of any other MD software package that is capable of running simulations on arbitrary molecules without having to "piece together" a force field for each molecule?<br><br>Thanks,<br><br>Nancy<br><br>
<br><br><br><div class="gmail_quote">On Fri, Jul 31, 2009 at 4:53 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5"><br>
<br>
Nancy wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
I am trying to run a MD simulation on trehalose (glucose disaccharide) in water. I obtained the PDB file from the URL: <a href="http://www.rcsb.org/pdb/files/ligand/TRE_model.pdb" target="_blank">http://www.rcsb.org/pdb/files/ligand/TRE_model.pdb</a> . When I run pdb2gmx on the PDB file:<br>
<br>
pdb2gmx -f TRE_model.pdb -o TRE_model.gro -v<br>
<br>
I chose force field 5 (OPLS) from the list:<br>
<br>
Select the Force Field:<br>
0: GROMOS96 43a1 force field<br>
1: GROMOS96 43a2 force field (improved alkane dihedrals)<br>
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br>
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)<br>
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)<br>
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>
6: [DEPRECATED] Gromacs force field (see manual)<br>
7: [DEPRECATED] Gromacs force field with hydrogens for NMR<br>
8: Encad all-atom force field, using scaled-down vacuum charges<br>
9: Encad all-atom force field, using full solvent charges<br>
<br>
And I received the following error message:<br>
<br>
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.0.5<br>
Source code file: pdb2gmx.c, line: 429<br>
<br>
Fatal error:<br>
Atom C1 in residue TRP 1 not found in rtp entry with 24 atoms<br>
while sorting atoms<br>
-------------------------------------------------------<br>
<br>
</blockquote>
<br></div></div>
Well, pdb2gmx thinks that TRE is tryptophan, so it's looking to complete a TRP building block. Furthermore, your procedure is undoubtedly going to fail. Force fields and pdb2gmx are not magic; they are not equipped to handle any arbitrary molecule you may want to simulate. None of the force fields provided with Gromacs will contain information for trehalose by default. There is information for glucose in some of the force fields (check the .rtp files), and you may be able to piece trehalose together from that information.<br>
<br>
Otherwise, you will have to go through the *very difficult and time-consuming* process of parameterization:<br>
<br>
<a href="http://oldwiki.gromacs.org/index.php/Parameterization" target="_blank">http://oldwiki.gromacs.org/index.php/Parameterization</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
Please help.<br>
<br>
<br>
Thank you,<br>
<br>
Nancy<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br></div>
------------------------------------------------------------------------<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 <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<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>
<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 <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote></div><br>