<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language:EN-US">Previously,
something like happened to me, the solution that worked for me was to use acpype
(code.google.com/p/acpype) and Amber FF. In this way, you could rule out
problems related to the prodrg parameters.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language:EN-US"><br></span></p><p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language:EN-US">Best
regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language:EN-US"><br></span></p><p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language:EN-US">Aldo<o:p></o:p></span></p><br><div><div><p align="right" style="text-align:left;"><font class="Apple-style-span" color="#FFFF00" face="Arial" size="2"><b><i></i></b></font></p><p class="MsoNormal"><font class="Apple-style-span" color="#FFFF00" face="Arial" size="2"><b><i><span class="apple-style-span"><span style="font-size:10.0pt;line-height:115%;color:black;">=======================================</span></span><span style="font-size:10.0pt;line-height:115%;color:black;"><br><span class="apple-style-span">Aldo Segura-Cabrera</span><br><span class="apple-style-span">Laboratorio de Bioinformática</span><br><span class="apple-style-span">Centro de Biotecnología Genómica</span><br><span class="apple-style-span">Instituto Politécnico Nacional</span><br><span class="apple-style-span">Blvd. Del
Maestro esquina Elías Piña, 88710</span><br><span class="apple-style-span">Reynosa, Tamaulipas, México.</span><br><span class="apple-style-span">(899)9243627 ext. 87747</span><br><span class="apple-style-span">e-mail:</span><span class="apple-converted-space"> </span><span class="apple-style-span"><a rel="nofollow" target="_blank" href="mailto:asegurac@ipn.mx"><span style="color:#0658B5;">asegurac@ipn.mx</span></a>;</span><span class="apple-converted-space"> </span><span class="apple-style-span"><a rel="nofollow" target="_blank" href="mailto:aldosegura@gmail.com"><span style="color:#0658B5;">aldosegura@gmail.com</span></a></span><br><span class="apple-style-span">=========================================</span></span></i></b></font></p></div></div><br><br>--- El <b>jue 28-abr-11, Justin A. Lemkul <i><jalemkul@vt.edu></i></b> escribió:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left:
5px;"><br>De: Justin A. Lemkul <jalemkul@vt.edu><br>Asunto: Re: [gmx-users] simulation with ligand at the active site<br>A: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Fecha: jueves, 28 de abril de 2011, 1:02<br><br><div class="plainMail"><br><br>onetwo wrote:<br>> Hello Users,<br>> <br>> I have a query regarding simulation with the ligand.<br>> <br>> In my protein there are two ligands, one of them (coenzyme) is from the<br>> crystal data, and other I have docked at the active site, while docking<br>> it is showing good interaction with all the active site residues very<br>> well.<br>> I used GROMOS96 43a1 force field, and got the topology file made from<br>> prodrg beta, using GROMOS 96.1 for both the ligands.<br><br>PRODRG produces notoriously bad topologies. See, for instance:<br><br><a href="http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips"
target="_blank">http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips</a><br><br>> while doing equilibration I did, brendenson coupling on like<br>> ; Berendsen temperature coupling is on in two groups<br>> Tcoupl = V-rescale<br>> tc-grps = Protein Non-Protein<br>> tau_t = 0.1 0.1<br>> ref_t = 300 300<br>> <br>> and in MD simulation also<br>> ; Berendsen temperature coupling is on in two groups<br>> Tcoupl = V-rescale<br>> tc-grps = Protein Non-Protein<br>> tau_t = 0.1 0.1<br>> ref_t = 300 300<br>> <br><br>There could be some debate about these settings, and I do not know the best way to handle temperature coupling. It seems to me that if you have a ligand (or multiple) bound to a protein, the interactions between the protein and ligand(s) will be tightly coupled, such that you shouldn't lump the ligands into the "Non-Protein" group, which in this case likely comprises solvent. Maybe someone
with more experience in these types of simulations can share some insight.<br><br>> But after 1ns equibiration, one of the ligand (the one which I docked)<br>> is going away from the active site and then I ran it for 4 ns further,<br>> it has gone more far from the cavity. Following is the link to the snapshot of the ligand at different time.<br>> <br>> <a href="https://picasaweb.google.com/118389174994698260649/Md_complex?authkey=Gv1sRgCMis2qry3cGj7AE#5600499037480314402" target="_blank">https://picasaweb.google.com/118389174994698260649/Md_complex?authkey=Gv1sRgCMis2qry3cGj7AE#5600499037480314402</a><br>> <br>> I want to ask if the change in the<br>> position of ligand is justified with the parameters i have taken or it<br>> if i have done something wrong?<br>> <br><br>Without providing the actual topology(ies) of the ligand(s) and a complete .mdp file, it is hard to say. But if you're using PRODRG output, I would
suspect that it would be the culprit.<br><br>-Justin<br><br>> Thanks and Regards<br>> <br>> <<a href="http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle" target="_blank">http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle</a>?><br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (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>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a
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