[gmx-users] CHARMM nonbonded parameters and grompp output

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 21 17:27:10 CET 2008

Justin A. Lemkul wrote:
> 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.
Urey bradley is implemented. CHeck manual.

> 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
> ========================================
> 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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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