Re: [gmx-users] Re: Segmentation Fault using g_cluster

2013-09-06 Thread Tsjerk Wassenaar
Hi Evelyne, I haven't got a clue... But does it work if you use -settime when concatenating the trajectories, to avoid having frames with the same time index? It shouldn't cause a segfault, but it might. Cheers, Tsjerk On Fri, Sep 6, 2013 at 7:20 AM, deplazes e.depla...@uq.edu.au wrote: Hi

[gmx-users] Re: Segmentation Fault using g_cluster

2013-09-06 Thread deplazes
You're a genious. It works! Thanks a lot From: Tsjerk Wassenaar [via GROMACS] ml-node+s5086n5011009...@n6.nabble.commailto:ml-node+s5086n5011009...@n6.nabble.com Date: Fri, 6 Sep 2013 02:12:25 -0700 To: Evelyne Deplazes e.depla...@uq.edu.aumailto:e.depla...@uq.edu.au Subject: Re: Segmentation

[gmx-users] Re: Segmentation Fault using g_cluster

2013-09-06 Thread deplazes
You also need to make a new index file that corresponds to the new , reduced .tpr file Cheers E Enjoy Ausserberg From: Tsjerk Wassenaar [via GROMACS] ml-node+s5086n5011009...@n6.nabble.commailto:ml-node+s5086n5011009...@n6.nabble.com Date: Fri, 6 Sep 2013 02:12:25 -0700 To: Evelyne Deplazes

Re: [gmx-users] Re: Segmentation Fault using g_cluster

2013-09-06 Thread Tsjerk Wassenaar
Hi Evelyne, So I was reading carelessly... I didn't notice you used an index file with trjcat. If you later try to use the same index file, that may indeed cause a segfault. Good that it works now. Cheers, Tsjerk On Fri, Sep 6, 2013 at 12:29 PM, deplazes e.depla...@uq.edu.au wrote: You also

[gmx-users] Setting multiple coordination distances in constrained system

2013-09-06 Thread Alexander Björling
Dear users, I have a dimeric protein system, where I would like to define two pairwise sidechain-sidechain distances, one in each monomer. I'd like to do this back and forth, so that I can alternately enforce long (~0.6nm) and short (~0.3nm) distances, and follow the response of the protein. I

[gmx-users] Seeking solution for the error Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms.

2013-09-06 Thread Santhosh Kumar Nagarajan
Hi guys, My problem is in the first step itself. Fatal error: Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms. I understand that the problem is with the .rtp database. But. My doubt is how to create a new rtp entry for that missing residue. The

Re: [gmx-users] Seeking solution for the error Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms.

2013-09-06 Thread Justin Lemkul
On 9/6/13 8:52 AM, Santhosh Kumar Nagarajan wrote: Hi guys, My problem is in the first step itself. Fatal error: Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms. I understand that the problem is with the .rtp database. But. My doubt is how to

Re: [gmx-users] simulation explode while switching from NVT to NPT

2013-09-06 Thread Golshan Hejazi
Dear Rafael, Thanks for your reply. Yes, I did follow the link. This means that the system is not equilibrated well. I tried to perform some more minimization but it seems that steepest decent have already minimized it well.  Therefore I decided to perform MD at lower T. I tried 5ns of NVT

[gmx-users] Help on itp and pdb

2013-09-06 Thread R R S Pissurlenkar
If I use the topology and coordinates of a small molecule from ATB for docking (structure.pdb / structure.itp which match in atom numbering and sequence); after docking and saving the structure_dock.pdb, the atom numbering does not match the numbering in the structure.itp file. This causes

[gmx-users] Atom ordering for RB dihedrals in OPLS-AA

2013-09-06 Thread prateekj
Hi, I am trying to build itp file for polymer simulations using OPLS-AA and had two questions I could not find a clear answer from the forum or the manual. 1. Is the order of bond types listed in a row of the [dihedral] section important, i.e. if I replace ijkl by lkji, will this make any

Re: [gmx-users] NMR restrained MD

2013-09-06 Thread Rama Krishna Koppisetti
Sorry ..,here are my distance restraints file: [ distance_restraints ] ;ai ajtypeindextype'low up1up2fac 3012679 1 0 1 0.0 1.62142.2111.0 3012696

Re: [gmx-users] NMR restrained MD

2013-09-06 Thread Justin Lemkul
On 9/6/13 5:23 PM, Rama wrote: Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data. Without restraints there is no problem, but if I include distance restraints in topology file, getting fatal error: the lipid atom index # was not

Re: [gmx-users] Help on itp and pdb

2013-09-06 Thread Justin Lemkul
Please don't reply to the entire digest; the archive is hopelessly confused as it is, but let's not make it any worse ;) On 9/6/13 2:29 PM, R R S Pissurlenkar wrote: If I use the topology and coordinates of a small molecule from ATB for docking (structure.pdb / structure.itp which match in

Re: [gmx-users] NMR restrained MD

2013-09-06 Thread Justin Lemkul
On 9/6/13 5:27 PM, Rama Krishna Koppisetti wrote: Sorry ..,here are my distance restraints file: Without context as to what these numbers are, there's little useful information here. I suspect you're trying to implement restraints between protein and lipid atoms, which will not work for

[gmx-users] NMR restrained MD

2013-09-06 Thread Rama
Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data. Without restraints there is no problem, but if I include distance restraints in topology file, getting fatal error: the lipid atom index # was not recognized by using this command: g_grompp

Re: [gmx-users] Atom ordering for RB dihedrals in OPLS-AA

2013-09-06 Thread Justin Lemkul
On 9/6/13 2:11 PM, prateekj wrote: Hi, I am trying to build itp file for polymer simulations using OPLS-AA and had two questions I could not find a clear answer from the forum or the manual. 1. Is the order of bond types listed in a row of the [dihedral] section important, i.e. if I replace

Re: [gmx-users] NMR restrained MD

2013-09-06 Thread Rama Krishna Koppisetti
H i Justin, Thanks for your reply. How to do that? On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:23 PM, Rama wrote: Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data. Without restraints there

Re: [gmx-users] NMR restrained MD

2013-09-06 Thread Justin Lemkul
On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote: H i Justin, Thanks for your reply. How to do that? If .rtp entries exist for your lipid with the force field, it's simply a matter of pdb2gmx -merge, choosing which chains should be written as a single [moleculetype]. If the lipids are

Re: [gmx-users] NMR restrained MD

2013-09-06 Thread Justin Lemkul
On 9/6/13 5:56 PM, Rama Krishna Koppisetti wrote: Hi Justin , Is there any script available in gromacs documentation or some where? My guess is no. Ask Google. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of

Re: [gmx-users] NMR restrained MD

2013-09-06 Thread Rama Krishna Koppisetti
Hi Justin , Is there any script available in gromacs documentation or some where? Thanks On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote: H i Justin, Thanks for your reply. How to do that? If .rtp entries

Re: [gmx-users] simulation explode while switching from NVT to NPT

2013-09-06 Thread Justin Lemkul
On 9/6/13 12:48 PM, Golshan Hejazi wrote: Dear Rafael, Thanks for your reply. Yes, I did follow the link. This means that the system is not equilibrated well. I tried to perform some more minimization but it seems that steepest decent have already minimized it well. Therefore I decided to