[gmx-users] Cys-Cys bonding

Dear Users and masters! I know that gromacs can prepare the topology with covalent bonding of cys-cys bridges in the individual chain on fly. However, when two different chains are connected with such bonds and the intital geometry is satisfactory (distance, angle) It doesn't work. It was done

[gmx-users] secondary structure element constraining

Yes, it does... Should I follow this advices http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints ? Phi/Psi lines are like in the sample, with only changed values of atom indexes and angles, measured with pymol of gromacs tools ai ajakal | type | label | phi |

[gmx-users] secondary structure element constraining

degree of oscilation) less appropriate methods? or simple genrestr with 1 kJ forces ? Thank You! On 6/10/18 3:04 AM, alex rayevsky wrote: >* Dear users! *>>* Did anybody meet the problem of positional constraints applied to the *>* secondary structure, namely keeping the 310-heli

[gmx-users] secondary structure element constraining

Dear users! Did anybody meet the problem of positional constraints applied to the secondary structure, namely keeping the 310-helix stable all the time? I've modelled the substructure - a bundle of alpha helices with a 310 helix segment (longer, thinner, reactive) on the one of them. And I need

[gmx-users] Electric field or CompEl protocol?

, it is a solid idea, but I think this algorithm is clunky and how it agrees with PBC is unclear to me. If you get clean and reasonable data, please let everyone know! :) Alex On 5/20/2018 1:16 AM, alex rayevsky wrote: >* Dear Alex! *>>* Yes, I thought about all Your reflections and I'm also

Re: [gmx-users] Electric field or CompEl protocol?

e simulated fields can be incompatible with what's being studied. My response probably doesn't help much, but this is the situation with all MD software that relies on Ewald summation. Alex On 5/19/2018 5:16 PM, alex rayevsky wrote: Dear all, Which protocol, Electric field section or the CompEl, I should

[gmx-users] Electric field or CompEl protocol?

Dear all, Which protocol, Electric field section or the CompEl, I should use in the situtation: 1. I built an ion channel by homology, prepared a bilayer membrane, embeded my protein and run a simulation to relax the system (100 ns) 2. my channel was closed all the time. 3. I want to run four

[gmx-users] (no subject)

Dear all, How to modify a mdp file to generate two different tpr files, from the same initital coordinates of a Na 1.5 voltage gated channel in the membrane (it is already relaxed and in a closed state)? I need to set parameters for the system with a voltage of -80 mV and than, after 100 ns start

Re: [gmx-users] ion channel in lipid bilayer

! >>>> ___ Kroon, P.C. Sun, 18 Feb 2018 15:52:30 -0800 <https://www.mail-archive.com/search?l=gromacs.org_gmx-users@maillist.sys.kth.se=date:20180218> Hi Alex, Try either insane.py, or charmm-gui. I can't provide links, since I'm on my phone. You may need to generate the topol

[gmx-users] Fwd: ion channel in lipid bilayer

I'm sorry for repeat, but nobody answered the question and I decided to duplicate the request. Maybe it is a problem with a form of question or its content, please, point me the mistake. Hi all! I have a question concerning immersion of the ion channel (four subunits with extracellular domains

[gmx-users] ion channel in lipid bilayer

Hi all! I have a question concerning immersion of the ion channel (four subunits with extracellular domains and a bundles of helixes) into the lipid bilayer. 6 years ago I used some tutorial or mailing lists, which described the way from KALP15 tutor. With CCR5 model there were no problems at

[gmx-users] (no subject)

Dear users and developers! I have a question about replica exchange sampling and simulation annealing method. Well, I have a protein (TubulinG) X-ray, however it lack last 10-11 residues, which are probably exposured to the solvent (and it seems are flexible enough to be invisible for X-ray). The