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
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