[gmx-users] OPLS to gromos96 problems

Magnus Andersson magnus.andersson at chembio.chalmers.se
Wed Jan 4 15:06:15 CET 2006


I encountered this problem some time ago. I had some xtal waters in the
.pdb file from which I removed the hydrogens (after getting that same
error message) and the pdb2gmx worked fine.


> Hello All,
> I've successfully built .gro and .top files for a large riboprotein in
> OPLSAA using GROMACS. The problem is that it is so large I really need
> to use a UAFF to keep this computationally tractable. I tried running
> pdb2gmx and received errors such as
> "WARNING: atom H21 is missing..."
> I entered the missing hydrogens to the .hdb file and fixed this.
> However this brought forth two additional problems:
> ------------------------------------------------------------------------
> QUESTION 1) long bonds, there must be thousands
> eg
> Warning: Long Bond (74318-75599 = 13.2452 nm)
> Warning: Long Bond (74345-75599 = 13.5764 nm)
> Several questions: What do the atom numbers refer to? The input ".gro"
> file numbering? The uncompleted output .gro file? Also, I'd say with
> the exception of ~25 Long Bonds they are all between some atom and atom
> #75599. I find this confusing since I'm using a GROMACS .gro file as
> input. Are there any suggestions as to what this might mean?
> ------------------------------------------------------------------------
> QUESTION 2) "Fatal error: Atom H211 not found in rtp database in
> residue GUA, it looks a bit like H21"
> I assume that this is due to the fact that I have >10,000 atoms in my
> system and the atom type and atom number columns are merging. GUA is
> the first nucleotide after 10,000 atoms and the atomtype and number
> appear thusly for the H21 atom in this residue:
> H2110013
> Is there a way to have GROMACS accept H21 rather than exiting? If this
> is not the case do I need to go back to the .pdb files to get around
> this problem?
> Many thanks, as always,
> Ken
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