[gmx-users] Ligand-ligand Tutorial

Hi, Anyone know any ligand- ligand tutorial? I've been trying to set up a taurine  simulation with lysophosphatidylcholines (LPC) with no success. Thanks in Advance-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Hypericin interaction with DNA molecule

ing md ,i created an index file linking the DNA and Hypercin into on tc-grps and ran the simulation for 1 ns. Is it enough or it should  run longer? My PC is quadcore Q6600 with 2 gigs of ram. Thanks in advance Hovakim Grabski Russian Armenian (Slavonic) University Bionformatics Department-- gm

[gmx-users] System with 4 Hypericin Molecules in Water

Dear GROMACS users, I have been trying to set up a simulation system  containing  4 Hypericin molecules in a box of water. When I'm trying to run energy minimization,I get this error:   WARNING 1 [file HYP1_GMX.itp, line 5]:   Overriding atomtype CT WARNING 2 [file HYP1_GMX.itp, line 6]:   Over

[gmx-users] HBonds with VMD

s. Where is my mistake? Thanks in Advance Hovakim Grabski Russian-Armenian(Slavonic) University-- 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! P

[gmx-users] g_energy Kinetic Energy

x27;s about 5400 kJ/mol and for the second one is 28000 kJ/mol). I wonder if g_energy extracts the energy values from the whole system including the water molecules,and if it is so is there any way to extract the kinetic energy values  of the Hypericin molecules? Thanks in Advance Hovakim Gr

[gmx-users] HBonds between molecules

Dear Gromacs users, I ran a simulation with 13 Hypericin molecules in water for 10 ns and 7 of them formed an aggregate.Is there any way to find out between what molecules and atoms Hbonds were formed? Thanks in advance Hovakim Grabski Russian-Armenian(Slavonic) University -- gmx-users mailing

[gmx-users] DNA podophyllotoxin

bonds with the end of the DNA molecule. Could this happen because of the topology file? Thanks in advance Hovakim Grabski<>-- 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

[gmx-users] Hypericin dimer affinity

Dear Gromacs users, I set up a simulation of 4 Hypericin molecules for 5 ns. 2 of them formed a dimer. Is there any way to find the dissociation constant Kd  and bond energy  of Hypericin ? Thanks in advance Hovakim-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailm

[gmx-users] Umbrella Sampling Hypericin Dimer

Dear Gromacs users, I want to set up an umbrella sampling simulation of an Hypericin dimer. I have  created   position restraint files  for hypericin with genrestr and then use it  with the topology file, so I want to know if it is just restraining one of the Hypericin Molecules or both of them?

[gmx-users] Gromacs 4.6 GPU on Nvidia 250 GTS?

Dear Gromacs users, Is it possible to use GROMACS 4.6 GPU Mode on Nvidia 250 GTS? Thanks in advance, Hovakim  -- 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 be

[gmx-users] Intercalation DNA-Ethidium bromide

e's a sudden change. Is there any chance I could see intercalation? P.S.  Or I should create an artifical gap between dna bases and then set up a simulation? Thanks in advance, Best regards, Hovakim Grabski-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

[gmx-users] Hbonds between Adenine and Thymine

. How can I select Adenine from one strand and Thymine from the other strand and then run g_hbond ? Thanks in Advance Best regards, Hovakim Grabski -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

RE: [gmx-users] Hbonds between Adenine and Thymine

01  0.1858 -0.2851 -0.7312    17DT     C3' 1353   8.760   9.970   3.199  0.4414 -0.1050  0.1494    17DT     H3' 1354   8.659   9.970   3.158  0.9166  0.1514 -1.0617    17DT     C2' 1355   8.845   9.865   3.127  0.0046 -0.5079  0.2147    17DT    H2'1 1356   8.773   9.809   3.066  0

[gmx-users] Solvating Podophyllotoxin in ethanol

;PTOX.itp" ; Include ethanol topology #include "ETA.itp" Is there any way to fix it? Thanks in advance, Best regards, Hovakim Grabski Russian-Armenian(Slavonic) University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

[gmx-users] Ligand-Ligand interaction

Thanks in Advance Hovakim Grabski Russian-Armenian Slavonic University-- 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 pos

[gmx-users] energy groups for specific parts of the molecule

s for example)? Are there any tutorials? Thanks in advance, Hovakim Grabski Russia- Armenian(Slavonic) University -- 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 b