[gmx-users] CHARMM nonbonded parameters and grompp output

[Justin A. Lemkul]

Hi all,

As a number of others have attempted, I am exploring the use of the CHARMM force
fields in Gromacs.  I have read about a number of difficulties throughout the
list archive, but I am seeing something that thusfar it seems no one has
reported, regarding nonbonded parameters.  Let me tell you what I've done so
far, and perhaps someone can shed some light on what's going on.

I downloaded the ffcharmm* files from the old User Contribution site, following
a link I found in the archive.  I created a .hdb file (for ease of use) and
edited the .tdb files, as they contained some inconsistencies in atom naming
and formatting.  I converted the CHARMM27 force field parameters from Alex
MacKerell's site using a script that was also made available through User
Contributions, giving me ffcharmm.itp, ffcharmmbon.itp, and ffcharmmnb.itp.  So
far, so good.  For the moment, I am also approximating the Urey-Bradley
potential by using distance restraints, using scripts that came along with the
ffcharmm package.

I was able to produce a topology for hen egg white lysozyme (a decent system to
test, I thought), with correct disulfides, charges, etc. and life was good.  I
ran grompp to attempt an in vacuo energy minimization, and saw this among my
output:

processing topology...
Generated 0 of the 8646 non-bonded parameter combinations

The rest of the grompp output indicated no errors or warnings (aside from a net
charge, which is OK for now).  I reasoned that there should be _some_ form of
nonbonded interactions within the protein, correct?  I read about 1-4
interactions (i.e. OPLSAA generates these by scaling, so they are not
explicitly included in ffoplsaanb.itp), but such scaling is reportedly not used
in the CHARMM force field, and thus it was no surprise to find [ nonbond_params
] within ffcharmmnb.itp.  This brings me to my question: is grompp not finding
these parameters?  And if so, why?

I noticed that ffcharmmnb.itp is formatted much like the GROMOS force field
files (ffgmxnb.itp, ffG*nb.itp) and saw something that is not mentioned in the
manual.  The first line under [ atomtypes ] in each of the GROMOS force fields
has formatting like:

;name  at.num      mass        charge   ptype       c6           c12
    O    8      15.99940       0.000       A   0.22617E-02   0.74158E-06

The at. num column is not mentioned in the manual (Gromacs version 3.3).  Is it
needed for proper interpretation of the *nb.itp files?  Such a column is
missing in my ffcharmmnb.itp file.  The [ nonbond_params ] and [ pairtypes ]
sections seem to have correct formatting, so I am not sure that this
(potential) inconsistency among the [ atomtypes ] is causing the issue.

Thanks for reading (yet another) long email from me, and thanks in advance if
anyone has any ideas as to what's going on.

-Justin


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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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