[gmx-users] Ligand charge issues

Hi Gromacs users, I am studying the protein-ligand interaction using amber99sb-ILDN force field in gromacs 4.6.2. To create the ligand topology (lipid A), I have used online version of ACPYPE/antechamber.http://webapps.ccpn.ac.uk/acpype/ I have read a lot more time that charge on different atoms

[gmx-users] mdp file help

Hi guys, I'm new to Gromacs and seeking some input on my .mdp file for the production run. I want to perform simulation to check protein stability over time and the after that the stable protein will be used for protein-protein docking/interactions. I'm using cubic box (with 1nm pbc) with water

[gmx-users] disallowed residue calculation

Dear gmx users, Is there any gmx command to plot the number of residues in disallowed region of the Ramachandran plot. g_rama and xrama doesnot have such options to calculate the same. -Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational

[gmx-users] defining 2 posres at a time in mdp

same mdp file simultaneously. regards anwar - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [

[gmx-users] Re: water molecules in vacuum simulation

1000 1000 12502 1 1000 1000 1000 12405 1 1000 1000 1000 #endif regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and

[gmx-users] Re: water molecules in vacuum simulation.

Hi all, I am performing in vacuum simulation of a protein containing crystallographic water molecules. I want to constrain these water molecules, but pdb2gmx program doesnot generate the pr.itp for water molecules. How do I constrain these water molecules. regards Anwar

[gmx-users] water molecules in vacuum simulation.

Dear users, Is it possible to perform an invacuum simulation with few constrained water molecules? I dont want to use the explicit solvent, but want to use the crystallographic water molecules in protein and perform invacuum simulation. regards Anwar -- Mohd Anwaruddin

[gmx-users] Re: invacuo minimization

Hi David, I have checked the mdout.mdp and as you said it has pbc = xyz. What do I do now. I havent run editconf, but why it is taking pbc conditions? How do I remove these?? thanks Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational

[gmx-users] invacuo minimization

= no gen_vel = no Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext

[gmx-users] invacuo simulation

simulation seem to be equilibrated for a certain time and then but again they start deviating. I dont have any clue for why the system is showing a lot of discrepancies with in different simulations when they differ only in the box size. Can some on through some light on it? regards Anwar

[gmx-users] theory of MD

. Kindly give me the references for papers and tutorials. with best wishes Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel

[gmx-users] Re: gmx-users Digest, Vol 28, Issue 63

hi maria, So, what parameters do I have to give in the mdp file for periodic boundary condictions, I thought just by applying the PBC through editconf will do the job. regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and

[gmx-users] periodic boundary condition

Dear users, I want to apply the periodic boundary condition. So, the following options are sufficient or not? editconf_d -f xxx.gro -o xxx_box.gro -d 1.0 -c Or do we also have to give the option -pbc regards Anwar -- Mohd Anwaruddin Project Assistant C/o

[gmx-users] invcuo and solvent simulation

Dear users, What are parameters which differs in invacuo and water simulation apart from that water is not added in invacuo. I mean what are the things we have to be considered or not considered while performing invacuo simulation. regards Anwar -- Mohd Anwaruddin Project

[gmx-users] regarding comm_mode

in I can find how the dynamics is performed internally. thanks in advance regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076

[gmx-users] comm_mode

performed internally. thanks in advance regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70

[gmx-users] Re: gmx-users Digest, Vol 28, Issue 28

t around 5 A. There are no drasrtic structural changes seen. However, I think it is better if I run the dynamics without pressure coupling as you have suggested. Give me suggestions. regards Anwar In addition to Erik and my suggestions, you should also remove the overall rotation: comm_mode=l

[gmx-users] vacuum simulation problem

= isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 kindly guide me in this issue. regards Anwar -- Mohd

[gmx-users] Vacuum simulation problem

at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 kindly guide me in this issue. regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting

[gmx-users] adding new residue (MSE) in topology database

can I calculate them. thanks in advance Anwar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [

[gmx-users] adding new residue (MSE) in topology database

calculate them. thanks in advance Anwar - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROT

[gmx-users] adding new residue (MSE) in topology database

calculate them. thanks in advance Anwar - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [