[gmx-users] Visualization problem of bromo atom connected to an aromatic ring due to gromacs or VMD?
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 1opls_145 1 DRG C1 1 -0.018 13.0190 2opls_729 1 DRG C2 10.002 12.0110 3opls_730 1 DRGBR1 10.016 79.9040 4opls_166 1 DRG C3 20.149 12.0110 5opls_167 1 DRG O1 2 -0.174 15.9994 6opls_168 1 DRGHAA 20.066 1.0080 7opls_145 1 DRG C4 2 -0.020 13.0190 8opls_145 1 DRG C5 2 -0.021 13.0190 9opls_145 1 DRG C6 30.002 12.0110 10 opls_136 1 DRG C7 30.093 14.0270 11 opls_139 1 DRG C8 30.172 12.0110 12 opls_750 1 DRG N1 3 -0.267 14.0067 13opls_154 1 DRG O2 4 -0.108 15.9994 14opls_155 1 DRGHAB 40.108 1.0080 15 opls_235 1 DRG C9 50.395 12.0110 16 opls_236 1 DRG O3 5 -0.664 15.9994 17 opls_237 1 DRG N2 50.159 14.0067 18 opls_240 1 DRGHAD 50.024 1.0080 19 opls_136 1 DRGC10 50.086 14.0270 20 opls_206 1 DRGC11 60.000 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-al...@h-da.de Tel.: ++49-(0)6151-168406 http://www2.h-da.de/cub/index.php?id=177 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Visualization problem of bromo atom connected to an aromatic ring due to gromacs or VMD?
Meyer-Almes, Franz-Josef, Prof. Dr. wrote: 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: Simply changing the atom types is not likely an appropriate solution. OPLS-AA is an all-atom force field, in which all H should be represented. You have a grand total of 3 H atoms in this structure. After a quick look at your structure, this is definitely not correct. Also note that the charges that PRODRG generates fall somewhere between marginal and totally incorrect for even the GROMOS force fields. snip 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. I don't see how the problem is with Gromacs - you say that the output of mdrun is reasonable. If you've defined a bond between two atoms, the bond will be there. The topology is correct, VMD's interpretation of the molecule has no such guarantee. If it is a problem with VMD, Is there a remedy for the incorrect visualization of the drug molecule? VMD guesses where bonds should be based on inter-atomic distances. There may be ways around this effect. Many have been mentioned on this list, so a few minutes of poking around in the archive should turn up some useful information. There may also be some information in the VMD mailing list archive or in the VMD manual. -Justin Thank you in advance, Franz F.-J. Meyer-Almes Hochschule Darmstadt Fachbereich Chemie- und Biotechnologie Schnittspahnstr. 12 64287 Darmstadt Email: franz-josef.meyer-al...@h-da.de Tel.: ++49-(0)6151-168406 http://www2.h-da.de/cub/index.php?id=177 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
