[gmx-users] Visualization problem of bromo atom connected to an aromatic ring due to gromacs or VMD?
Meyer-Almes, Franz-Josef, Prof. Dr.
franz-josef.meyer-almes at h-da.de
Sun Sep 12 20:07:47 CEST 2010
Dear all,
I have two question:
1) Are the atom types I chose for the use of OPLS force field correct?
I use gromacs 4.0.7 with opls force field under Ubuntu Linux to simulate enzyme drug interaction. Since the Dundee Prodrg Server converts PDB files of drug structures just in an .itp file compatible with gromos forcefields, I had to change the atom types as follows:
drug.itp:
[ moleculetype ]
; Name nrexcl
drug 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 opls_145 1 DRG C1 1 -0.018 13.0190
2 opls_729 1 DRG C2 1 0.002 12.0110
3 opls_730 1 DRG BR1 1 0.016 79.9040
4 opls_166 1 DRG C3 2 0.149 12.0110
5 opls_167 1 DRG O1 2 -0.174 15.9994
6 opls_168 1 DRG HAA 2 0.066 1.0080
7 opls_145 1 DRG C4 2 -0.020 13.0190
8 opls_145 1 DRG C5 2 -0.021 13.0190
9 opls_145 1 DRG C6 3 0.002 12.0110
10 opls_136 1 DRG C7 3 0.093 14.0270
11 opls_139 1 DRG C8 3 0.172 12.0110
12 opls_750 1 DRG N1 3 -0.267 14.0067
13 opls_154 1 DRG O2 4 -0.108 15.9994
14 opls_155 1 DRG HAB 4 0.108 1.0080
15 opls_235 1 DRG C9 5 0.395 12.0110
16 opls_236 1 DRG O3 5 -0.664 15.9994
17 opls_237 1 DRG N2 5 0.159 14.0067
18 opls_240 1 DRG HAD 5 0.024 1.0080
19 opls_136 1 DRG C10 5 0.086 14.0270
20 opls_206 1 DRG C11 6 0.000 14.0270
21 opls_083 1 DRG S1 7 -1.000 32.0600
Drug.gro:
PRODRG COORDS
21
1DRG C1 1 8.555 5.270 -3.838
1DRG C2 2 8.529 5.317 -3.967
1DRG BR1 3 8.392 5.231 -4.068
1DRG C3 4 8.602 5.424 -4.019
1DRG O1 5 8.580 5.472 -4.145
1DRG HAA 6 8.507 5.419 -4.189
1DRG C4 7 8.700 5.485 -3.941
1DRG C5 8 8.725 5.438 -3.812
1DRG C6 9 8.653 5.331 -3.760
1DRG C7 10 8.681 5.281 -3.619
1DRG C8 11 8.788 5.172 -3.616
1DRG N1 12 8.913 5.205 -3.598
1DRG O2 13 8.945 5.341 -3.583
1DRG HAB 14 9.044 5.351 -3.570
1DRG C9 15 8.736 5.032 -3.632
1DRG O3 16 8.619 5.004 -3.652
1DRG N2 17 8.828 4.932 -3.624
1DRG HAD 18 8.925 4.956 -3.626
1DRG C10 19 8.790 4.792 -3.610
1DRG C11 20 8.903 4.690 -3.629
1DRG S1 21 8.838 4.520 -3.654
1.11480 1.11480 1.11480
2) Visualization problem of VMD?
The second question is related to the first one:
I use VMD 1.8.7 under Windows XP. When I try to visualize above mentioned Drg.gro file using VMD, the bromo atom appears as a tiny point and is not connected to C2 as it should. When I convert the Drg.gro file to a pdf-file by the command editconf, the pdf-structure displays the bromo atom correctly connected to the aromatic ring. In addition, during the course of an mdrun over 1 ns the relative position and the distance of the bromo atom to C2 remained unchanged. The distance between BR1 and C2 in the final mdrun after some relaxation was constantly 1.89 Angstrom which is realistic. Is my observation a visualization problem of VMD or a serious problem with gromacs which I do not see.
If it is a problem with VMD, Is there a remedy for the incorrect visualization of the drug molecule?
Thank you in advance,
Franz
F.-J. Meyer-Almes
Hochschule Darmstadt
Fachbereich Chemie- und Biotechnologie
Schnittspahnstr. 12
64287 Darmstadt
Email: franz-josef.meyer-almes at h-da.de
Tel.: ++49-(0)6151-168406
http://www2.h-da.de/cub/index.php?id=177
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