On 10/09/2011 10:23 AM, Sandeep Somani wrote:
Hi Mark
It worked ! pdb2gmx is now properly processing the pdb, and moreover
the potential energy from gmx is within 1.27 kJ/mol of that from
Charmm. More on energy comparison shortly.
However, further tinkering of the rtp and pdb file was
Hi Mark
Thanks for the rtp definitions. I added the rtp defs to aminoacids.rtp and
renamed residue and atom names in pdb file.
But pdb2gmx is still complaining about the terminal groups. It seems to have
picked up ACE, but not CT3.
pdb2gmx error message and modified pdb file are listed below.
On 09/09/11, Sandeep Somani ssom...@gmail.com wrote:
Hi Mark
Thanks for the rtp definitions. I added the rtp defs to aminoacids.rtp and
renamed residue and atom names in pdb file.
But pdb2gmx is still complaining about the terminal groups. It seems to have
picked up ACE, but
Hi Mark
It worked ! pdb2gmx is now properly processing the pdb, and moreover the
potential energy from gmx is within 1.27 kJ/mol of that from Charmm. More on
energy comparison shortly.
However, further tinkering of the rtp and pdb file was required to generate
the topology:
1.
The original rtp
Hi
I am trying to set up a simulation for dialanine using charmm27 ff but am
getting errors in pdb2gmx due to missing definitions in rtp file.
I created the pdb file (below) using Charmm for the sequence
ACE-ALA-ALA-CT3.
pdb2gmx recognizes ALA atoms but not those of the terminal groups ACE and
On 9/09/2011 8:05 AM, Sandeep Somani wrote:
Hi
I am trying to set up a simulation for dialanine using charmm27 ff but
am getting errors in pdb2gmx due to missing definitions in rtp file.
I created the pdb file (below) using Charmm for the sequence
ACE-ALA-ALA-CT3.
pdb2gmx recognizes ALA
Hi,
I am seeking help in creating the .pdb file for a dialanine
molecule using the databank. I have the parameters for a single alanine
molecule. how do i go from here.
Thanks
Debashis
___
gmx-users mailing listgmx-users@gromacs.org
Hi Debashis,
Parameters and .pdb file are different things. To generate a structure
for dialanine you can use prodrg, pymol, write it by hand or search the
web. If you want to use your own force field parameters you have to
write a .itp file. Check the gromacs manual for that.
TsjerkOn 6/8/06,
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