[gmx-users] OPLSAANR RNA problems

David spoel at xray.bmc.uu.se
Fri Oct 21 21:22:52 CEST 2005

On Fri, 2005-10-21 at 14:41 -0400, 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.

The hdb format has changed since this force field was uploaded. With 3.3
you have to specify the base name for the generated hydrogens as well.

> 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
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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://xray.bmc.uu.se/~spoel

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