[gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites?

[blau]

Hi Bjorn, This is still the recommended procedure. Contact me directly if you need help with the conversion to an rtp file.Best, Christian
-------- Original message --------From: Bjorn Wesen <bjorn.wesen at gmail.com> Date: 27/03/2020  17:16  (GMT+01:00) To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] SARS-CoV-2 main protease with ligand from acpype,
 	but converting to vsites? Hi list, I have a working sim of the solvated SARS-CoV-2 main proteasedimer fromhttps://www.rcsb.org/structure/6Y84using amber99sb-ildn and pdb2gmx-generated vsites for speed, and wanted toproceed by adding some of the various proposed inhibitor ligands to the simfor further workflow testing, for example, this one:"COCCOc1cc(C(=O)N=c2[nH][nH]c(C)c2-c2ccc(Cl)cc2)ccn1".So I made a pdb of this and generated a .gro and .itp through one of theonline Acpype servers (the one at http://bio2byte.be/acpype ), but there isno option to generate gmx vsites for getting rid of the hydrogenbond-angles so I simply assume the result will blow up when running withthe longer timesteps the rest of the sim now uses.I found a 5 year old post on this list with the same problem, with thisadvice from Justin:https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-October/101732.html"At present, the simplest way forward is to take the information you havein yourligand topology from acpype and create an .rtp entry, then allow pdb2gmx toprocess the whole thing and build the virtual sites on the ligand."I was wondering, is this still the recommended method? I'm notsuper-knowledgeable in the details of how to port something from the ITP tothe RTP formats. Should I just give up on doing it this way or is it an"opportunity to learn the details" ;) Or is there a better way. Maybe someother gmx tool to build the vsites for a ligand without having to go allthe way by creating the rtp stuff.Also, yes, I could simply give up the vsites and run everything slower.This is the fallback. Maybe some of these ligands simply won't work wellwith these constructions at any rate.Regards/Bjorn-- Gromacs Users mailing list* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists* For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.