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
>
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>
>
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Received on Wed Jun 07 2017 - 12:30:03 PDT
