Re: [gmx-users] ions different

2008-03-18 Thread Mark Abraham
> Dear experts, > I have done upto minimization but faults in equilibration I am again > starting the minimization, now in adding ions of sodium the following > error is given, what is the reason for this. > Warning: atom names in topol.top and ions.pdb don't match (NA - Na) > Warning: atom names i

[gmx-users] ions different

2008-03-18 Thread s lal badshah
Dear experts, I have done upto minimization but faults in equilibration I am again starting the minimization, now in adding ions of sodium the following error is given, what is the reason for this. Warning: atom names in topol.top and ions.pdb don't match (NA - Na) Warning: atom names in topol.to

[gmx-users] Remove COM of group only in x & y direction

2008-03-18 Thread Mirijanian, Dina Tigranui
Hello, I need to be able to remove the COM motion of a defined group only in x-direction and y-direction but not the z-direction. Is there a way to do this in GROMACS? The comm_mode options removes ALL components of the COM motion of the defined group. Thank you. _

Re: [gmx-users] How to create three different zones to minimize energy of a enzyme?

2008-03-18 Thread Mark Abraham
Evanildo Júnior wrote: Dear gmx-users, I would like to minimize the potential energy of the active site of an enzyme. Because I do not have too much computer power to perform a full enzyme calculation, I need to create three different zones in which the calculation will take place. The first

Re: [gmx-users] g_anaeig

2008-03-18 Thread Mark Abraham
SWAPNA wrote: > Dear gmx users, > I am using g_anaeig to filter my traj along the first eigenvector. > > 'g_anaeig -b 5000 -f 15000 -v eigenvec.trr -f calpha.tpr -s calpha.xtc > -first 1 -last 1 -filt alongeigvec1 -dt 100' > 5000ps to 15000ps has equilibriated trajectory. So I am using that to >

[gmx-users] center of mass removal

2008-03-18 Thread baloilgiullare
Hi all, searching in the ml I found this thread: http://www.gromacs.org/pipermail/gmx-users/2006-April/021256.html about comm-mode=angular and the method described in J. Chem. Phys. 112(1) pp. 9-23 to remove com translation and rotation. I was not able to download the modified versions of the co

[gmx-users] How to create three different zones to minimize energy of a enzyme?

2008-03-18 Thread Evanildo Júnior
Dear gmx-users, I would like to minimize the potential energy of the active site of an enzyme. Because I do not have too much computer power to perform a full enzyme calculation, I need to create three different zones in which the calculation will take place. The first one is the outer boun

[gmx-users] RE: gmx-users Digest, Vol 47, Issue 58

2008-03-18 Thread Evanildo Júnior
rs mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't

Re: [gmx-users] g_anaeig

2008-03-18 Thread SWAPNA
Dear gmx users, I am using g_anaeig to filter my traj along the first eigenvector. 'g_anaeig -b 5000 -f 15000 -v eigenvec.trr -f calpha.tpr -s calpha.xtc-first 1 -last 1 -filt alongeigvec1 -dt 100' 5000ps to 15000ps has equilibriated trajectory. So I am using that to perform essential dynamics. W

[gmx-users] Definition of mol2 file used by topolbuild

2008-03-18 Thread Bruce Ray
Apparently, my documentation for topolbuild is not sufficiently precise in the definition of the input molecular structure file. The program, topolbuild, is described as taking a mol2 file as input. By mol2 file, I mean a syntactically correct mol2 file with Tripos atom types and charges, and wit

Re: [gmx-users] Black whole simluations

2008-03-18 Thread Maik Goette
Thank you Sir If this was fake or not...Me and my dear colleagues had a good laugh, anyway...also about the nice comments. Maybe this inspires: http://www.youtube.com/watch?v=qiSkyEyBczU "Black hole sun, won't you come" Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical

[gmx-users] nstcomm value

2008-03-18 Thread avinash kumar
Hello all, I am simulating pressure driven flow in a nanochannel. To introduce a pressure gradient in the system I have put all the liquid atoms in one group and applied acceleration to it. Also I am periodically removing the centre of mass motion my nstcomm value. My doubt is that when

RE: [gmx-users] Force field

2008-03-18 Thread Ángel Piñeiro
Hi Nihar, unfortunately I can't help you with thioflavin parameterization and probably other people here will address you to general links. Our CDs were built on the base of topologies for smaller sugars already available in the gromos force field (pasting building blocks). I hope someone else can

Re: [gmx-users] average structure with ligand

2008-03-18 Thread Ran Friedman
Dear Anna, Use make_ndx to create any group you find useful. Ran. Anna Marabotti wrote: > Dear gmx-users, > I would like to create from my trajectory an average structure of my protein > with its ligand inside. > With both g_rmsf and g_cluster I am prompted to indicate one group, but > ligand

RE: [gmx-users] average structure with ligand

2008-03-18 Thread #NGUYEN CONG TRI#
Dear Anna, I think you can use make_ndx to make a new group for your ligand+protein. For example: $make_ndx -f filename.gro -o filename.ndx It will list all of the groups in you filename.gro file. Then select your protein and ligand and make a new name for the group. Use your filename.ndx ind

RE: [gmx-users] Force field

2008-03-18 Thread Dr. Niharendu Choudhury
Hi Ángel, Thanks a lot for coming forward. Regarding CD (\alpha, \beta and \gamma) I will contact you as soon as possible. For the moment I would like to get the same for Thioflavin-T. It is a fairly big molecules with I think 39 atoms. Can you tell me how go about (procedure in detail) to get t

[gmx-users] average structure with ligand

2008-03-18 Thread Anna Marabotti
Dear gmx-users, I would like to create from my trajectory an average structure of my protein with its ligand inside. With both g_rmsf and g_cluster I am prompted to indicate one group, but ligand and protein are separated into different groups, and I'd want to exclude water from this structure,