Hi Tom !!!
Can you guide to incorporate the AMBER parameter for ATP (
http://www.pharmacy.manchester.ac.uk/bryce/amber#cof) in ffamber. I am using
ffamber for the simulation of Protein + ATP.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Thu, Jan 21, 2010 at 7:06 PM, Thomas Piggot wrot
Thanks everyone,
you were right, it doesn't work if I only take off one phosphate from GTP. I
was using the wrong parameters, now I have an integer total charge.
Carla
On Thu, Jan 21, 2010 at 2:36 PM, Thomas Piggot wrote:
> If using an amber forcefield and GTP/GDP you can use the parameters on t
If using an amber forcefield and GTP/GDP you can use the parameters on
the following website. I have used the ATP/ADP ones and have had no
problems with many different systems and ATP/ADP conformations with
which I used to test these parameters.
http://www.pharmacy.manchester.ac.uk/bryce/amber
Carla Jamous wrote:
Thank you Justin,
but I ran a simulation before this one with GTP & it worked fine. GDP &
GTP parameters are identical except for GDP having less atoms.
This is why I can't understand why I don't get an integer charge while I
did in my previous simulation.
OK, but this
Carla Jamous skrev:
Thank you Justin,
but I ran a simulation before this one with GTP & it worked fine. GDP
& GTP parameters are identical except for GDP having less atoms.
This is why I can't understand why I don't get an integer charge while
I did in my previous simulation.
Carla
Well, if
Carla Jamous skrev:
Hi,
In order to run my simulation, I had to insert GDP parameters in
ffamber94 (the force field I'm using).
However, I'm having a problem with GDP charge.
the charge of every charge group in top file should be an integer. But
I'm getting a decimal charge which gives me nat
Thank you Justin,
but I ran a simulation before this one with GTP & it worked fine. GDP & GTP
parameters are identical except for GDP having less atoms.
This is why I can't understand why I don't get an integer charge while I did
in my previous simulation.
Carla
On Thu, Jan 21, 2010 at 2:15 PM, J
On 1/21/10 2:12 PM, Carla Jamous wrote:
Hi,
In order to run my simulation, I had to insert GDP parameters in
ffamber94 (the force field I'm using).
However, I'm having a problem with GDP charge.
the charge of every charge group in top file should be an integer. But
I'm getting a decimal charge w
Carla Jamous wrote:
Hi,
In order to run my simulation, I had to insert GDP parameters in
ffamber94 (the force field I'm using).
However, I'm having a problem with GDP charge.
the charge of every charge group in top file should be an integer. But
I'm getting a decimal charge which gives me n
Hi,
In order to run my simulation, I had to insert GDP parameters in ffamber94
(the force field I'm using).
However, I'm having a problem with GDP charge.
the charge of every charge group in top file should be an integer. But I'm
getting a decimal charge which gives me naturally a decimal total ch
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