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?
On Sun, Nov 7, 2010 at 4:49 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
hengame fallah wrote:
Hi,
I'm using the OPLS force field.
[ PHE ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_149 -0.005 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG 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 -0.115 7
HZ opls_146 0.115 7
C opls_235 0.500 8
O opls_236 -0.500 8
I want to attach "CL" atom instead of HZ
i made my pdb but when i use pdb2gmx, it adds HZ automatically
in gro and top files.
What should i do to get rid of this HZ and attach CL instead.
If the .rtp entry says to build PHE with those constituent atoms,
it will do so. You can make a custom .rtp entry that has CL
instead of HZ.
(I edited top and gro files and remove HZ from them, it seemed
to work properly at first, but when i tried to do energy
minimization, it had errors in top file
and i realized that it couldn't recognized the bond between
CL and CZ):
ERROR 1 [file topol.top, line 150]:
No default Bond types
ERROR 2 [file topol.top, line 422]:
No default Angle types
ERROR 3 [file topol.top, line 423]:
No default Angle types
All of these errors indicate that OPLS cannot accommodate such a
species. Making ad hoc changes to the topology often does this.
Look at what these lines contain and you will be able to identify
the relevant parameters that are missing.
<snip>
66 opls_401 5 CL CL 26 -1
35.453 ; qtot -1.06
I would seriously question the validity of doing this. Is it
really correct to put (essentially) a Cl- ion on a Phe ring and
call it correct? Proper parameterization is a very challenging
task, and I doubt what you've proposed here is valid.
http://www.gromacs.org/Documentation/How-tos/Parameterization
-Justin
...
[ bonds ]
...
59 66 1
60 61 1
60 62 1
63 64 1
63 65 1
...
[ angles ]
...
58 57 59 1
55 59 57 1
55 59 66 1
57 59 66 1
45 60 61 1
45 60 62 1
61 60 62 1
64 63 65 1
...
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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