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.we...@gmail.com>
Date: 27/03/2020 17:16 (GMT+01:00) To:
gromacs.org_gmx-users@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-requ...@gromacs.org.
--
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.
