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-- Jason M. Swails > On Jun 7, 2017, at 3:22 PM, Miguel Rivera <miguelrivera1855.gmail.com> wrote: > > Is there a paper or manual out there that can show me how to remove the > left over Cmap params? > >> On Fri, May 5, 2017 at 12:29 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote: >> >> Hi, >> >> I've been working on this for a bit, and I think I've got it figured >> out. There are a few errors here going on behind the scenes having to >> do with cpptraj and parmed. >> >> The problem is that currently parmed and cpptraj (which are what do >> the topology/trajectory heavy lifting respectively for MMPBSA.py) >> leave behind some extra stuff after stripping CHAMBER topologies. In >> the case of parmed it leaves behind some CMAP grids. When cpptraj then >> tries to read this topology it gets confused (since there is no >> CMAP_COUNT section) and exits with an error. On the other hand, >> cpptraj leaves behind some extra 1-4 Lennard-Jones parameters, which >> in turn confuses parmed. >> >> I'm currently fixing the behavior of cpptraj in GitHub: >> https://github.com/Amber-MD/cpptraj (now testing, should be done >> soon). >> >> I am also attaching a ligand topology file that should work for you. I >> tested it on the files you provided and it seems to work fine. >> However, make sure you verify that it gives you reasonable results! I >> have not tested it extensively beyond making sure nothing is obviously >> broken and it is possible further bugs lurk. I'll be doing more >> testing in the meantime. >> >> FYI this was the ante-mmpbsa.py command line I used: >> >> ante-MMPBSA.py -p step5_charmm2amber.parm7 -n ":277" -s >> ":POPC,WAT,CLA" -c complex.parm7 -r receptor.parm7 -l ligand.parm7 >> >> I then used the updated cpptraj to generate a new ligand topology from >> the original topology (see below for comments on this). I also had to >> use a custom mask for mmpbsa.py input to ensure that POPC and CLA were >> stripped as well, e.g. >> >> strip_mask = ":WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL, >> POPC,CLA", >> >> Just one further comment here on your cpptraj usage: >> >> On Fri, Apr 28, 2017 at 6:12 PM, Miguel Rivera >> <miguelrivera1855.gmail.com> wrote: >>> I decided to create .parm7 files using cpptraj tool. With scripts that >> look >>> like this: >>> >>> trajin prod.nc 1 1 1 >>> strip :TIP3 outprefix strip >>> strip :CLA outprefix strip >>> strip :POPC outprefix strip >> >> The number of strip commands here is overkill. If all you want is to >> keep residue 277 just use the "not" ("!") operator so you strip >> everything that is not residue 277: >> >> strip !:277 outprefix strip >> >> And if your intent is to just create a stripped topology, you can just >> use 'parmstrip': >> >> parm step5_charmm2amber.parm7 >> parmstrip !:277 >> parmwrite out cpptraj.ligand.parm7 >> >> Hope this helps, >> >> -Dan >> >> PS - Instead of using cpptraj to create the ligand topology, you can >> probably just remove the extra CHARMM_CMAP_PARAMETER sections from the >> ante-mmpbsa.py ligand topology file. >> >> -- >> ------------------------- >> Daniel R. Roe >> Laboratory of Computational Biology >> National Institutes of Health, NHLBI >> 5635 Fishers Ln, Rm T900 >> Rockville MD, 20852 >> https://www.lobos.nih.gov/lcb >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> >> > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Jun 14 2017 - 13:30:04 PDT