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
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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
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
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
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]
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
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.
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
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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
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
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?
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
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
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
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
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gmx-users mailing list
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
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
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
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
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