[gmx-users] Re: OPLSAANR RNA problems

[David]

On Sat, 2005-10-22 at 14:14 +0400, Andrey V. Golovin wrote:
> Hello Ken
> problem is that you can not use this forcefield with gromacs 3.3 only 
> gromacs 3.2.1, it is becouse gromacs 3.3 use different format for hdb 
> file (hydrogen database) and etc. I hope we will update our files to new 
> format.
> So you can install gromacs 3.2.1, create topology using pbd2gmx from 
> version 3.2.1 and do rest of stuff  using version 3.3
> goodluck, Andrey

Andrey, do you have any publications related to this force field? That
would strengthen the credibility and we could then consider adding it to
the default gromacs forcefield files.


> 
> Ken Rotondi wrote:
> > Hello all,
> > 
> > I am trying, not successfully, to simulate a RNA-protein complex in 
> > GROMACS. At the suggestion of David van der Spoel I tried using the 
> > oplsaanr forcefield found variant that includes nucleotides on the 
> > GROMACS  topologies page:
> > 
> > http://www.gromacs.org/topologies/force_fields.php
> > 
> > I downloaded and installed these files and ran pdb2gmx on my .pdb file, 
> > which failed with a fatal error:
> > -------------------------------------------------------
> > Program pdb2gmx, VERSION 3.3_beta_20050202
> > Source code file: h_db.c, line: 85
> > 
> > Fatal error:
> > wrong format in input file ffoplsaa.hdb on line
> >         2       7       OW
> > -------------------------------------------------------
> > 
> > I opened the .hdb for the standard opls ff .hdb and found water 
> > hydrogens defined thusly:
> > 
> > 2    7    HW    OW
> > 
> > Changing the .hdb in the oplsaanr to this removes this error.
> > 
> > This is confusing, since the manual (section 5.5.2) states that the 
> > first control atom (OW in the nr, HW in standard) is ALWAYS (emphasis 
> > mine) the atom to which the H atoms are connected.  Based upon this 
> > definition I would determine that the format the failed is correct and 
> > the format the works is incorrect, since the water hydrogen is bonded to 
> > the water oxygen (OW) and not the water hydrogen (HW). What am I missing?
> > 
> > To make matters more confusing, the gromos96.hdb uses the first format, 
> > which is correct by the manual, but fails when running the OPLSFF.
> > 
> > So I don't understand why the change fixes this or indeed what the 
> > problem is to begin with. Once this is fixed in the working oplsaanr.hdb 
> > the program progresses to this error:
> > -------------------------------------------------------
> > Program pdb2gmx, VERSION 3.3_beta_20050202
> > Source code file: ter_db.c, line: 85
> > 
> > Fatal error:
> > Reading Termini Database: expected 3 items of atom data in stead of 1 on 
> > line
> >         N      opls_287   14.0027    -0.3000
> > -------------------------------------------------------
> > 
> > What does this mean? As far as I can tell each line contains the atom 
> > name, type, mass and charge for atom, since I assume (dangerous) that 
> > the name (N in this case) is not atom data, while type, weight and 
> > charge are, there are indeed 3 items of atom data in this line? 
> > Comparing the ffoplsaa-n.tdb file with the ffoplsaanr-n.tdb finds them 
> > identical.
> > 
> > Is there anyone out there that has had success simulating RNA-protein 
> > complexes in GROMACS? If so, could you please give me a hand, suggest 
> > appropriate forcefields to use and allow me to e-mail you with some 
> > questions?
> > 
> > Sorry for the long post,
> > 
> > Ken
> > 
> > 
> > K.S. Rotondi Ph.D.
> > Research Fellow
> > The Gierasch Laboratory
> > Department of Biochemistry and Molecular Biology
> > University of Massachusetts-Amherst
> > Phone: 413-545-1250
> > Fax;      413-545-3291
> > 
> 
> 
-- 
David.
________________________________________________________________________
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://xray.bmc.uu.se/~spoel
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