Dear Mark,
I think that i couldn't explain my problem clearly, however i have changed
my .rtp but i don't know how should be my .hdb file.
a) The structure of *BOC* is: *-CO-CH2-CH(C6H5Cl)-CH2-NH-*
b) This is the new charges:
[ BOC ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.080 1
HA1 opls_140 0.060 1
HA2 opls_140 0.060 1
CB opls_149 0.055 2
HB opls_140 0.060 2
CG1 opls_145 -0.115 2
CD1 opls_145 -0.115 3
HD1 opls_146 0.115 3
CD2 opls_145 -0.115 4
HD2 opls_146 0.115 4
CE1 opls_145 -0.115 5
HE1 opls_146 0.115 5
CE2 opls_145 -0.115 6
HE2 opls_146 0.115 6
CZ opls_145 1.000 7
Cl opls_264 -1.000 7
CG2 opls_071 -0.120 8
HG1 opls_140 0.060 8
HG2 opls_140 0.060 8
C opls_235 0.700 9
O opls_236 -0.700 9
c) charge for CG1 in PHE (in OPLS .rtp) is negative, too.
d) Would you explain for me that what is wrong in my atom types?
e) As you see in the error, at first there are 63 residues (like my pdb) but
when when it adds COO- and NH3+ there are 69 residues! it should add only
one "O" (for COO-) and two "H"s for (NH3+) i think.
There are 1 chains and 0 blocks of water and 3 residues with 63 atoms
chain #res #atoms
1 ' ' 3 63
All occupancy fields zero. This is probably not an X-Ray structure
Opening library file /usr/share/gromacs/top/ffoplsaa.atp
Atomtype 1
Reading residue database... (ffoplsaa)
Opening library file /usr/share/gromacs/top/ffoplsaa.rtp
Residue 57
Sorting it all out...
Opening library file /usr/share/gromacs/top/ffoplsaa.hdb
Opening library file /usr/share/gromacs/top/ffoplsaa-n.tdb
Opening library file /usr/share/gromacs/top/ffoplsaa-c.tdb
Back Off! I just backed up topol.top to ./#topol.top.3#
Processing chain 1 (63 atoms, 3 residues)
There are 3 donors and 3 acceptors
There are 4 hydrogen bonds
Checking for duplicate atoms....
Opening library file /usr/share/gromacs/top/specbond.dat
7 out of 7 lines of specbond.dat converted succesfully
N-terminus: NH3+
C-terminus: COO-
Now there are 3 residues with 69 atoms
Making bonds...
Warning: Long Bond (53-54 = 0.334847 nm)
Warning: Long Bond (53-56 = 0.334912 nm)
Warning: Long Bond (64-65 = 0.271173 nm)
Warning: Long Bond (64-66 = 0.347808 nm)
Warning: Long Bond (64-67 = 0.31288 nm)
Opening library file /usr/share/gromacs/top/aminoacids.dat
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.7
Source code file: ../../../../src/kernel/add_par.c, line: 233
Fatal error:
Atom HB1 not found in rtp database in residue BOC, it looks a bit like HB
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