[gmx-users] editconf (protein+bilayer)

Dear all I have a pdb of my protein. I want to position of protein in x,y and z relative to the bilayer .how can i do by editconf? rhanks Shape Yahoo! in your own image. Join our Network Research Panel

Re: [gmx-users] editconf (protein+bilayer)

mahbubeh zarrabi wrote: Dear all I have a pdb of my protein. I want to position of protein in x,y and z relative to the bilayer .how can i do by editconf? rhanks editconf -h (always a good start) editconf -translate -n

[gmx-users] Problem in genion

Hello, I am facing a problem while trying to neutralize my molecule. My molecule is a protein and after writing input file[.tpr] on seeing a charge of 6.0e+ i am trying to neutralize it by using 6 CL- ions. when i have tried 'genion' for small molecules it was running fine,but for this

Re: [gmx-users] Problem in genion

C.RAMYA wrote: Hello, I am facing a problem while trying to neutralize my molecule. My molecule is a protein and after writing input file[.tpr] on seeing a charge of 6.0e+ i am trying to neutralize it by using 6 CL- ions. when i have tried 'genion' for small molecules it was running

Re: [gmx-users] Problem in genion

Hi Ramya, don't forger to search the archive at http://www.gromacs.org/search before posting. As David said, it looks like that old genion+ gcc4.series compiler problem. (I also had it) Try compiling with Intel, gcc-3,gcc-2.96. Have a nice day. On 6/6/07, David van der Spoel [EMAIL PROTECTED]

Re: [gmx-users] Problem in genion

hello, OS is fedora 5 Compiler is cpp how can this be sorted out?? Thanks. C.RAMYA wrote: Hello, I am facing a problem while trying to neutralize my molecule. My molecule is a protein and after writing input file[.tpr] on seeing a charge of 6.0e+ i am trying to neutralize

Re: [gmx-users] Problem in genion

C.RAMYA wrote: hello, OS is fedora 5 Compiler is cpp how can this be sorted out?? gcc -v if it says 4.1.x your machine is affected and you need to get another compiler or use the cvs 3.3 release code. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David.

Re: [gmx-users] Problem in genion

C.RAMYA wrote: hello, OS is fedora 5 Compiler is cpp cpp is a pre-processor http://en.wikipedia.org/wiki/C_preprocessor, not a compiler. Mark ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] request for help to prepare a 111 gold surface

Hi, I am trying to start a simulation involving self-assembly of protein on Au (111) surface where 111 designates the miller indices of the plane. I know how to construct a FCC lattice and the coordinates of a system using Fortran code. But I have no clue of how to get the coordinates of

[gmx-users] g_msd and make_ndx

Hello, I am looking to measure the diffusion coefficient of a subset of water molecules moving through a pore in a lipid bilayer. In looking at g_msd and the -mol option, the manual states that my index file needs references to molecule numbers rather than atom numbers. I was wondering how

[gmx-users] pdb files

Dear Gromacs users, Could you please help me to find pdb files for glyceric acid esters cyanamide phosphatidylcholine glyceroyl thioesters tetrose polyglyceric acid hemiacetal Thank you in advance - Moody friends. Drama queens. Your life?

Re: [gmx-users] pdb files

Sagittarius wrote: Dear Gromacs users, Could you please help me to find pdb files for glyceric acid esters cyanamide phosphatidylcholine glyceroyl thioesters tetrose polyglyceric acid hemiacetal Thank you in advance You build these yourself using a molecule building program. I don't know

[gmx-users] g_hbond (method)

Dear all, I would like to know the actual cut-off angle used by gromacs package to calculate Hydrogen bond. since in User manual of version 3.2 and earlier, it was written á equal to or lesser than áHB = 60 degree While in User manual of version 3.3, it is mentioned as á equal to or lesser

Re: [gmx-users] pdb files

Dear Mark Abraham Thank you very much for your help. Could you please help me to find such a not free molecule building program. Maybe it will be useful anyway somehow. Thank you in advance. Mark Abraham [EMAIL PROTECTED] wrote: Sagittarius wrote: Dear Gromacs users, Could you

Re: [gmx-users] pdb files

Dear Mark Abraham Thank you very much for your help. Could you please help me to find such a not free molecule building program. Maybe it will be useful anyway somehow. Start with a Google search. Mark ___ gmx-users mailing list

RE: [gmx-users] pdb files

This site can have some: http://alpha2.bmc.uu.se/hicup/ Welcome to HIC-Up, the Hetero-compound Information Centre - Uppsala, a freely accessible resource for structural biologists who are dealing dealing with hetero-compounds (small molecules). Catch ya, Dr. Dallas Warren Lecturer Department

Re: [gmx-users] g_hbond (method)

Anil Kumar wrote: Dear all, I would like to know the actual cut-off angle used by gromacs package to calculate Hydrogen bond. since in User manual of version 3.2 and earlier, it was written á equal to or lesser than áHB = 60 degree While in User manual of version 3.3, it is mentioned as á

Re: [gmx-users] pdb files

Dallas B. Warren wrote: This site can have some: http://alpha2.bmc.uu.se/hicup/ Welcome to HIC-Up, the Hetero-compound Information Centre - Uppsala, a freely accessible resource for structural biologists who are dealing dealing with hetero-compounds (small molecules). otherwise molden or

Re: [gmx-users] using old energies

lorix wrote: Hi everyone, I am simulating proteins in water at the equilibrium. I try to run new simulations with a short protein (deleting atoms from the previous .gro file). I understood that gromacs stores the atom velocities in the .gro file but also in the .edr file! I would like to use