Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber.

From: Daniel Roe <>
Date: Fri, 5 May 2017 14:29:08 -0400


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
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: (now testing, should be done

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 command line I used: -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 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
<> wrote:
> I decided to create .parm7 files using cpptraj tool. With scripts that look
> like this:
> trajin 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,


PS - Instead of using cpptraj to create the ligand topology, you can
probably just remove the extra CHARMM_CMAP_PARAMETER sections from the ligand topology file.

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852

AMBER mailing list

Received on Fri May 05 2017 - 11:30:03 PDT
Custom Search