> Sorry i'm probably being a bit slow, but i can't see where the "bond-type"
> atom names/types don't correspond with the opls-xxx names from the
> ffoplsbon.atp and ffoplsbon.rtp files for use with the ffoplsbon.itp file
> names.
The header for ffoplsaanb.itp is
[ atomtypes ]
; full atom descrip
Sorry i'm probably being a bit slow, but i can't see where the "bond-type"
atom names/types don't correspond with the opls-xxx names from the
ffoplsbon.atp and ffoplsbon.rtp files for use with the ffoplsbon.itp file
names.
Tom
--On 03 December 2006 14:39 +1100 Mark Abraham <[EMAIL PROTECTED]>
> Hi,
>
> I don't see why it doesn't all work, can you not just use the
> ffoplsaanb.itp file to map the opls_xxx names to the ones used in
> ffoplsbon.itp?
Yeah, that's what I thought, but the second field in the nb.itp is
"bond-type" and doesn't correspond like you'd think they might.
Mark
___
Hi,
I don't see why it doesn't all work, can you not just use the
ffoplsaanb.itp file to map the opls_xxx names to the ones used in
ffoplsbon.itp?
Cheers
Tom
--On 03 December 2006 08:23 +1100 Mark Abraham <[EMAIL PROTECTED]>
wrote:
Komath Damodaran wrote:
Hi All,
I am trying to build
Komath Damodaran wrote:
Hi All,
I am trying to build the itp file for a molecule. I would like to use
the opls force field. The ffoplsaa.atp contains the atom types as
opls_xxx. But the ffoplsbon.itp which contains the bond-angle-dihedral
parameters does not use the opls_xxx convention. Is th
Dinesh Pinisetty wrote:
Hello,
I am curious to know if its possible to swap the co-ordinates in .gro
file, using GROMACS. I have a .gro file, now I want to swap 'x' and 'z'
co-ordinates keeping the 'y' coordinates same.
Now that I think about it, literally cut and paste is easiest... b
Justin Lemkul wrote:
Hello all,
I have a quick question regarding an MD simulation I am attempting to run
(again, the membrane protein which I had problems with previously). Thanks to
the helpful suggestions; my system is now well-minimized! The last step before
I would like to take before run
Dinesh Pinisetty wrote:
Hello,
I am curious to know if its possible to swap the co-ordinates in .gro
file, using GROMACS. I have a .gro file, now I want to swap 'x' and 'z'
co-ordinates keeping the 'y' coordinates same.
I really appreciate any suggestions.
sed was born for this k
Dinesh Pinisetty wrote:
Hello,
I am curious to know if its possible to swap the co-ordinates in .gro
file, using GROMACS. I have a .gro file, now I want to swap 'x' and 'z'
co-ordinates keeping the 'y' coordinates same.
I really appreciate any suggestions.
Sincerely,
Dinesh.
_
Hello,
I am curious to know if its possible to swap the co-ordinates in .gro
file, using GROMACS. I have a .gro file, now I want to swap 'x' and 'z'
co-ordinates keeping the 'y' coordinates same.
I really appreciate any suggestions.
Sincerely,
Dinesh.
__
The theory underlying this is reviewed in our group's 1995
Biophysical Journal (Chiu et al) paper where we introduced the
surface tension boundary conditions---a deeper look at the theory is
in in Steve White's earlier paper in PNAS that is referenced in our
'95 paper. The short answer is yes,
Ibrahim M. Moustafa wrote:
Hi gmx-users,
I have a little problem with gromacs-3.3.1 installed on a Mac-OSX.
After installation (either building the package myself as instructed, or
using a binary form GROMACS web site) I could not run any program with
just typing the name on the xterm!
for
toma0052 wrote:
Hello,
I have a question about calculating the surface tension for the
water-lipid interface of a lipid bilayer. After an MD run, I can use my .edr
file and g_energy to calculate the surface tension. I believe that the
surface tension is calculated something like gamma = (P
Dear all gmx-users,
I have been trying to dig out some well cited paper on
simulation of globular protein using PME .Can anyone
please suggest to me some references I can look out
for.
Thanks to all.
--
Dilraj Lama,
Graduate student,
Bioinformatics and Biomolecular Simualtion
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