[gmx-users] [ angle_restraints_z ]

Hi all, There are atoms (a1 and a2) in my small molecule coordinate file that have the same z component: a1: atom#22 (x1,y1,60.231) a2: atom#45 (x2,y2,60.231)If I use these lines only Therefore the vector a1-a2 makes theta=90o with the z-axis. in my previous MD runs the a1-a2 were flexible (the

Re: [gmx-users] How to build a custom protein (PDB file)

Ok! I will give them a shot! Thanks! -- ___ Ricardo O. S. Soares Post-graduation Student in Biological Physics University of Sao Paulo - USP Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP Phone: 55 (16) 3602-4840 Curriculum Lat

Re: [gmx-users] How to build a custom protein (PDB file)

Ricardo Soares skrev: Hello everyone! I have a particular amino acid sequence and I wanna build a custom-shaped protein and make it a pdb file (I'm talking about non-realistic forms, like squares or a full extended chain). Can anyone indicate me some software for this task? Thanx! I don't

Re: [gmx-users] How to build a custom protein (PDB file)

Quoting Ricardo Soares <[EMAIL PROTECTED]>: > Hello everyone! > > I have a particular amino acid sequence and I wanna build a > custom-shaped protein and make it a pdb file (I'm talking about > non-realistic forms, like squares or a full extended chain). Can anyone > indicate me some software for

[gmx-users] How to build a custom protein (PDB file)

Hello everyone! I have a particular amino acid sequence and I wanna build a custom-shaped protein and make it a pdb file (I'm talking about non-realistic forms, like squares or a full extended chain). Can anyone indicate me some software for this task? Thanx! --

Re: [gmx-users] trjorder problems

[EMAIL PROTECTED] wrote: Hi all: I am trying to know how many and which molecules of solvent are near my system, I read the manual and I found that one can do this using trjorder, but I can not do this with my Gromacs version 3.3.2 beacause in this version there is a problem and one can not use

[gmx-users] trjorder problems

Hi all: I am trying to know how many and which molecules of solvent are near my system, I read the manual and I found that one can do this using trjorder, but I can not do this with my Gromacs version 3.3.2 beacause in this version there is a problem and one can not use options -o and -r together

RE: [gmx-users] Ordering with trjorder

> From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Date: Fri, 16 May 2008 18:20:02 +0700 > Subject: [gmx-users] Ordering with trjorder > > Dear gmx_users, > > could you clarify me how the "trjorder" procedure works? > Manual says "For each frame of the trajectory the selected > molecul

[gmx-users] Ordering with trjorder

Dear gmx_users, could you clarify me how the "trjorder" procedure works? Manual says "For each frame of the trajectory the selected molecules will be reordered according to..." and so on. Does it mean that the ordering within each frame is INDEPENDENT on the prehistory and further moving of t

RE: [gmx-users] Semi-isotropic pressure coupling

Hi, You X-Y area does not change because your X-Y compressibility is ridiculously small. BTW does somebody know why certain emails on the mailing list have the personal email address set as reply-to, instead or the mailing list? Berk. > Date: Wed, 14 May 2008 11:18:37 -0400 > From: [EMAIL PR