Hi list, I have a working sim of the solvated SARS-CoV-2 main protease dimer from
https://www.rcsb.org/structure/6Y84 using amber99sb-ildn and pdb2gmx-generated vsites for speed, and wanted to proceed by adding some of the various proposed inhibitor ligands to the sim for 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 the online Acpype servers (the one at http://bio2byte.be/acpype ), but there is no option to generate gmx vsites for getting rid of the hydrogen bond-angles so I simply assume the result will blow up when running with the longer timesteps the rest of the sim now uses. I found a 5 year old post on this list with the same problem, with this advice 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 have in your ligand topology from acpype and create an .rtp entry, then allow pdb2gmx to process the whole thing and build the virtual sites on the ligand." I was wondering, is this still the recommended method? I'm not super-knowledgeable in the details of how to port something from the ITP to the 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 some other gmx tool to build the vsites for a ligand without having to go all the 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 well with 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 visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
