Anirban Ghosh wrote:
Thanks a lot Mark and Justin for your replies.
If PRODRG results have to be taken with a pinch of salt, then can you
please suggest me how to get the proper topology for my ligand, just
hints. In particular the .itp file is missing the HZ, HB2 and HB3
hydrogen atoms, which are present in the PDB and GRO files. But the
other hydrogen atoms are defined properly. Any suggestion is welcome.
The missing atoms are not there likely because they are not required. Please
see the following:
http://www.gromacs.org/Documentation/Terminology/Force_Fields/United_Atom_Force_Field
As for derivation of parameters:
http://www.gromacs.org/Documentation/How-tos/Parameterization
-Justin
Regards,
Anirban
On Mon, Nov 23, 2009 at 5:31 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Anirban Ghosh wrote:
Hi ALL,
I want to do a simulation of a protein in presence of a ligand
(L-DOPA). I am trying to obtain the topology of L-DOPA from the
PRODRG server. However I am getting an error in the number of
atoms in the PDB file (with all hydrogens) and the topology
parameter file. The PDB file consists of 25 atoms, but the itp
file gives definition for 22 atoms (3 hydrogens are missing). So
every time there is an error w.r.t. number of atoms mismatch.
This is happening because PRODRG gives GROMOS-compatible topologies.
They are united-atom. So naturally, if you attempt to use an
all-atom structure, there will be mismatch.
I also would not trust the PRODRG topology at face value, as I have
posted across this list dozens of times.
-Justin
----------------------------------------------------------------------------------------------------------------------------------------------------------------------
PDB:
TITLE Gnomes, ROck Monsters And Chili Sauce
MODEL 1
ATOM 1 N DAH 1 15.600 17.820 -3.200 1.00 0.00
ATOM 2 CA DAH 1 16.490 17.500 -2.040 1.00 0.00
ATOM 3 C DAH 1 18.010 17.580 -2.400 1.00 0.00
ATOM 4 O DAH 1 18.560 16.790 -3.210 1.00 0.00
ATOM 5 CB DAH 1 16.100 16.180 -1.290 1.00 0.00
ATOM 6 CG DAH 1 14.980 16.190 -0.220 1.00 0.00
ATOM 7 CD1 DAH 1 13.790 16.990 -0.410 1.00 0.00
ATOM 8 CD2 DAH 1 15.130 15.410 0.970 1.00 0.00
ATOM 9 CE1 DAH 1 12.770 16.990 0.570 1.00 0.00
ATOM 10 CE2 DAH 1 14.100 15.400 1.950 1.00 0.00
ATOM 11 CZ DAH 1 12.900 16.200 1.750 1.00 0.00
ATOM 12 OE2 DAH 1 14.280 14.630 3.070 1.00 0.00
ATOM 13 OZ DAH 1 11.880 16.230 2.690 1.00 0.00
ATOM 14 OXT DAH 1 18.680 18.630 -1.760 1.00 0.00
ATOM 15 HA DAH 1 16.330 18.300 -1.320 1.00 0.00
ATOM 16 HB2 DAH 1 15.790 15.470 -2.050 1.00 0.00
ATOM 17 HB3 DAH 1 17.000 15.790 -0.820 1.00 0.00
ATOM 18 HD2 DAH 1 16.020 14.820 1.110 1.00 0.00
ATOM 19 HE1 DAH 1 11.880 17.580 0.420 1.00 0.00
ATOM 20 HD1 DAH 1 13.670 17.590 -1.300 1.00 0.00
ATOM 21 HE2 DAH 1 15.190 14.330 3.110 1.00 0.00
ATOM 22 HZ DAH 1 11.550 15.340 2.820 1.00 0.00
ATOM 23 H1 DAH 1 15.920 18.680 -3.630 1.00 0.00
ATOM 24 H2 DAH 1 15.640 17.070 -3.880 1.00 0.00
ATOM 25 H3 DAH 1 14.650 17.930 -2.880 1.00 0.00
TER
ENDMDL
TOPOLOGY FILE:
[ moleculetype ]
; Name nrexcl
DAH 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 DAH O 1 -0.715 15.9994
2 C 1 DAH C 1 0.387 12.0110 3
OM 1 DAH OXT 1 -0.716 15.9994 4
CH1 1 DAH CA 1 0.178 13.0190 5 NL
1 DAH N 1 0.683 14.0067 6 H
1 DAH H2 1 0.010 1.0080 7 H 1
DAH H3 1 0.010 1.0080 8 H 1
DAH H1 1 0.011 1.0080 9 CH2 1
DAH CB 1 0.152 14.0270 10 C 1
DAH CG 2 -0.020 12.0110 11 CR1 1
DAH CD2 2 0.001 12.0110 12 HC 1
DAH HD2 2 0.019 1.0080 13 C 1
DAH CE2 3 0.130 12.0110 14 OA 1
DAH OE2 3 -0.197 15.9994 15 H 1
DAH HE2 3 0.051 1.0080 16 C 1
DAH CZ 3 0.130 12.0110 17 OA 1
DAH OZ 3 -0.197 15.9994 18 H 1
DAH HZ 3 0.051 1.0080 19 CR1 1
DAH CE1 3 0.001 12.0110 20 HC 1
DAH HE1 3 0.031 1.0080 21 CR1 1
DAH CD1 4 0.000 12.0110 22 HC 1
DAH HD1 4 0.000 1.0080
[ bonds ]...
-----------------------------------------------------------------------------------------------------------------------------------------------------------
How can I rectify this issue? Any suggestion is welcome. Thanks
a lot.
Regards,
Anirban
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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