[gmx-users] OPLSAANR RNA problems

Ken Rotondi ksr at chemistry.umass.edu
Fri Oct 21 20:41:02 CEST 2005

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:


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 

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 

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 

Sorry for the long post,


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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