On 9/11/2010 9:09 PM, hengame fallah wrote:
Dear Mark,
I edited my pdb like this:
...
ATOM 41 N BOC 3 -1.862 5.210 5.333
ATOM 42 H BOC 3 -2.325 4.344 5.618
ATOM 43 CA BOC 3 -1.001 5.232 4.169
ATOM 44 HA1 BOC 3 -0.540 6.235 4.026
ATOM 45 HA2 BOC 3 -0.172 4.511 4.360
ATOM 46 CB BOC 3 -1.797 4.794 2.924
ATOM 47 HB1 BOC 3 -2.244 3.809 3.204
ATOM 48 CG1 BOC 3 -2.976 5.730 2.589
ATOM 49 CD1 BOC 3 -1.231 3.466 0.845
ATOM 50 HD1 BOC 3 -2.070 2.790 1.081
ATOM 51 CD2 BOC 3 0.120 5.408 1.353
ATOM 52 HD2 BOC 3 0.357 6.277 1.986
ATOM 53 CE1 BOC 3 -0.471 3.236 -0.312
ATOM 54 HE1 BOC 3 -0.717 2.381 -0.964
ATOM 55 CE2 BOC 3 0.881 5.182 0.197
ATOM 56 HE2 BOC 3 1.706 5.870 -0.054
ATOM 57 CZ BOC 3 0.591 4.093 -0.639
ATOM 58 CG2 BOC 3 -0.935 4.544 1.698
ATOM 59 HG1 BOC 3 -3.530 5.331 1.707
ATOM 60 HG2 BOC 3 -3.708 5.729 3.431
ATOM 61 C BOC 3 -2.565 7.148 2.291
ATOM 62 O BOC 3 -2.716 8.035 3.131
ATOM 63 Cl BOC 3 1.525 3.816 -2.062
END
and my .rtp file for [ BOC ] is:
[ BOC ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B -0.005 1
HA1 opls_140 0.060 1
HA2 opls_140 0.060 1
CB opls_149 0.140 2
HB1 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 0.885 7
Cl opls_264 -1.000 7
CG2 opls_071 -0.005 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
[ bonds ]
N H
N CA
CA HA1
CA HA2
CA CB
CB HB1
CB CG1
CB CG2
CG1 CD1
CG1 CD2
CD1 HD1
CD1 CE1
CD2 HD2
CD2 CE2
CE1 HE1
CE1 CZ
CE2 HE2
CE2 CZ
CZ Cl
CG2 HG1
CG2 HG2
CG2 C
C O
-C N
and still i got that error!
Fatal error:
Atom HB11 not found in rtp database in residue BOC, it looks a bit
like HB1
a) This structure is phenylalanine with *two* backbone methylene
spacers, not the one you said in a previous email
b) Your charge groups are wrong (e.g. number 2)
c) Your charges are doubtful (CG1 is negative???)
d) Your atom types are worth checking (should the two backbone methylene
carbons have those types?)
e) The atom ordering of the coordinate file and .rtp file need to match
f) The atom coordinates do not correspond to the atom labels they are
given - presumably you got another bunch of "long bond" warnings that
you didn't include in your last email.
Mark
On Tue, Nov 9, 2010 at 1:12 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 9/11/2010 8:19 PM, hengame fallah wrote:
Thanks Justin,
actually the protein that i want to simulate consists of two
amino acids: PHE and BOC
BOC is an unusual amino acid as you know.
It has a Cl instead of HZ in PHE and has one extra CH2 in
comparison to PHE
So that probably means you'll have to pay care to the [bonds]
section in the .rtp file. The only bonds GROMACS knows about are
the ones in the .rtp. They have to be right. The errors below look
like you haven't done it right.
I finally defined a residue BOC in opls .rtp file:
[ BOC ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B -0.005 1
HA1 opls_140 0.060 1
HA2 opls_140 0.060 1
CB opls_149 0.140 2
HB1 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 0.885 7
Cl opls_264 -1.000 7
CG2 opls_071 -0.005 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
the ending part of my PDB is:
...
ATOM 38 HE2 PHE 2 -6.946 8.455 4.409
ATOM 39 CZ PHE 2 -5.456 10.015 4.624
ATOM 40 HZ PHE 2 -5.887 10.646 3.828
ATOM 41 N BOC 3 -1.862 5.210 5.333
ATOM 42 H BOC 3 -2.325 4.344 5.618
ATOM 43 CA BOC 3 -1.001 5.232 4.169
ATOM 44 HA1 BOC 3 -0.540 6.235 4.026
HA2 is missing here, per your .rtp
ATOM 45 CB BOC 3 -1.797 4.794 2.924
ATOM 46 HB1 BOC 3 -2.244 3.809 3.204
ATOM 47 CG1 BOC 3 -2.976 5.730 2.589
ATOM 48 CG2 BOC 3 -0.935 4.544 1.698
ATOM 49 CD1 BOC 3 -1.231 3.466 0.845
ATOM 50 HD1 BOC 3 -2.070 2.790 1.081
ATOM 51 CD2 BOC 3 0.120 5.408 1.353
ATOM 52 HD2 BOC 3 0.357 6.277 1.986
ATOM 53 CE1 BOC 3 -0.471 3.236 -0.312
ATOM 54 HE1 BOC 3 -0.717 2.381 -0.964
ATOM 55 CE2 BOC 3 0.881 5.182 0.197
ATOM 56 HE2 BOC 3 1.706 5.870 -0.054
ATOM 57 CZ BOC 3 0.591 4.093 -0.639
ATOM 58 C BOC 3 -2.565 7.148 2.291
ATOM 59 O BOC 3 -2.716 8.035 3.131
ATOM 60 CL BOC 3 1.525 3.816 -2.062
ATOM 61 HA2 BOC 3 -0.172 4.511 4.360
ATOM 62 HG1 BOC 3 -3.530 5.331 1.707
ATOM 63 HG2 BOC 3 -3.708 5.729 3.431
Now i got t this error:
...
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.69#
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 68 atoms
Making bonds...
Warning: Long Bond (52-53 = 0.334847 nm)
Warning: Long Bond (52-55 = 0.334912 nm)
Warning: Long Bond (63-64 = 0.271173 nm)
Warning: Long Bond (63-65 = 0.347808 nm)
Warning: Long Bond (63-66 = 0.31288 nm)
This is telling you the connectivity in your .rtp doesn't match
the spatial arrangement very well. Go back and check the .rtp file.
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 HB11 not found in rtp database in residue BOC, it looks a
bit like HB1
pdb2gmx is probably hopelessly confused by now. Fix the other
issues and try again.
Mark
-------------------------------------------------------
...
What should i do?
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