Discussion:
problem in hdb file
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Zuzana Benkova
2008-02-19 14:07:44 UTC
Permalink
Dear GMX users,
I want to prepare .gro and topology file starting from the .pdb file
for a polyethylene chain , whose residue is not defined in .rtp, .hdb.
and .tdb files. I have defined a new residue in ffoplsaa.rtp file as
follows

[ Eth ]
[ atoms ]
C1 opls_136 -0.120 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
C2 opls_136 -0.120 2
H21 opls_140 0.060 2
H22 opls_140 0.060 2
[ bonds ]
C1 H11
C1 H12
C1 C2
C2 H21
C2 H22
C2 +C1
In ffoplsaa.hdb I defined it as

Eth 2
2 6 H1 C1 C2 +C1
2 6 H2 C2 C1 -C2

At this point I have to note that the presence of the last control
atoms in this file has not influenced the process.
In ffoplsaa-n.tdb file I have added

[ Eth ]
[ replace ]
C2 opls_135 12.011 -0.18
[ add ]
3 4 H2 C2 C1
opls_140 1.008 0.06
[ delete ]
H21
H22

and in ffoplsaa-c.tdb file I have added

[ Eth ]
[ replace ]
C1 opls_135 12.011 -0.18
[ add ]
3 4 H1 C1 C2
opls_140 1.008 0.06
[ delete ]
H21
H22


After using pdb2gmx -f input.pdb I have obtained following message

Opening library file ffoplsaa.rtp
Opening library file
/usr/local/share/gromacs/gromacs-3.3/share/top/aminoacids.dat
Reading hexane.pdb...
Read 6 atoms
Opening library file
/usr/local/share/gromacs/gromacs-3.3/share/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 6 atoms
chain #res #atoms
1 ' ' 3 6
All occupancies are one
Opening library file
/usr/local/share/gromacs/gromacs-3.3/share/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
Residue 59
Sorting it all out...
Opening library file ffoplsaa.hdb
Error in hdb file: nah = 41
line = ''
Opening library file ffoplsaa-n.tdb
Opening library file ffoplsaa-c.tdb
Back Off! I just backed up topol.top to ./#topol.top.8#
Processing chain 1 (6 atoms, 3 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Checking for duplicate atoms....
Opening library file
/usr/local/share/gromacs/gromacs-3.3/share/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
N-terminus: Eth
C-terminus: Eth
Segmentation fault

Could you specify what means Error in hdb file: nah = 41
line = '' and what is the problem with segmentation.

My input structure in .pdb file is as follows

ATOM 1 C1 Eth 1 1.000 1.540 0.000
ATOM 2 C2 Eth 1 2.456 2.041 0.000
ATOM 3 C1 Eth 2 2.456 3.581 0.000
ATOM 4 C2 Eth 2 3.912 4.083 0.000
ATOM 5 C1 Eth 3 3.912 5.623 0.000
ATOM 6 C2 Eth 3 5.368 6.124 0.000
END

Thank you for help in advance
Best regards
Zuzana
Mark Abraham
2008-02-19 15:02:43 UTC
Permalink
Zuzana Benkova wrote:

Hi Zuzana,

Thanks for the clear description of what you are attempting to do.
Post by Zuzana Benkova
Eth 2
2 6 H1 C1 C2 +C1
2 6 H2 C2 C1 -C2
At this point I have to note that the presence of the last control atoms
in this file has not influenced the process.
They should - this is behaviour that the .hdb file should implement,
since it's analogous to adding an amino hydrogen to a peptide residue.
The problem that is occurring below is occurring at or before the
attempt by pdb2gmx to interpret these lines, so it's not too surprising
you don't observe any effect with the last control atom. You shouldn't
see any for the other control atoms either :-)
Post by Zuzana Benkova
Sorting it all out...
Opening library file ffoplsaa.hdb
Error in hdb file: nah = 41
line = ''
Opening library file ffoplsaa-n.tdb
Opening library file ffoplsaa-c.tdb
Back Off! I just backed up topol.top to ./#topol.top.8#
Processing chain 1 (6 atoms, 3 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Checking for duplicate atoms....
Opening library file
/usr/local/share/gromacs/gromacs-3.3/share/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
N-terminus: Eth
C-terminus: Eth
Segmentation fault
Could you specify what means Error in hdb file: nah = 41
line = '' and what is the problem with segmentation.
The error message is a bit cryptic. "nah" is an index variable that
meant that pdb2gmx had a problem reading what it thought was a potential
42nd residue hydrogen database entry. "line = ''" suggests that it found
a blank line. Probably the file format is intolerant of "spare" blank
lines, even at the end. The standard ffoplsaa.hdb only has about 35
entries, so clearly yours has been modified by more than just your one
residue above. If you can't see any problems in your copy of this file,
you'll need to provide us the last 50-odd lines of your ffoplsaa.hdb
file. Guessing wildly, you might have a problem with DOS vs Unix line
endings if you've edited this file on a Windows machine. You might try
the dos2unix utility to be sure this isn't the problem.

Segmentation faults refer to segmentation of memory in the computer.
When a programmer errs, or the user inputs data that the programmer
didn't anticipate but attempts to act on anyway (i.e. the programmer
errs :-)) then sometimes the program attempts to store/access data
to/from a memory location where that's not allowed. C programs tend to
die ungracefully at this point with the above message. GROMACS is
actually very good at not doing this without outputting something else
helpful on the way.

Thus, I think your .hdb file formatting is breaking pdb2gmx somehow. The
simplest solution is to keep pdb2gmx happy :-)

Mark

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