IC.
I just saw your previous thread.
thanks again for kind helps.
On 10/17/2012 08:49 PM, Justin Lemkul wrote:
On 10/17/12 2:46 PM, Albert wrote:
On 10/17/2012 08:43 PM, Justin Lemkul wrote:
Here you're adding atom types, not the associated GB parameters.
Some of
these atom types probabl
On 10/17/12 2:46 PM, Albert wrote:
On 10/17/2012 08:43 PM, Justin Lemkul wrote:
Here you're adding atom types, not the associated GB parameters. Some of
these atom types probably already exist within the gbsa.itp file of the force
field, judging by their names. At least one (OS) does not.
-
On 10/17/2012 08:43 PM, Justin Lemkul wrote:
Here you're adding atom types, not the associated GB parameters. Some
of these atom types probably already exist within the gbsa.itp file of
the force field, judging by their names. At least one (OS) does not.
-Justin
thank you for kind comment
On 10/17/12 2:41 PM, Albert wrote:
On 10/17/2012 08:35 PM, Justin Lemkul wrote:
You need GB parameters for every atom type in the system. Most protein and
nucleic acid types work out of the box, but if you have a complex system with
some novel molecule in it, you have to add parameters for th
On 10/17/2012 08:35 PM, Justin Lemkul wrote:
You need GB parameters for every atom type in the system. Most
protein and nucleic acid types work out of the box, but if you have a
complex system with some novel molecule in it, you have to add
parameters for the atom types that it uses.
thank
On 10/17/12 2:31 PM, Albert wrote:
Hello Justine:
I've got the following messages by command:
grompp -f implicit.mdp -c complex.pdb -p complex.top -o test.tpr
Setting gen_seed to 18463
Velocities were taken from a Maxwell distribution at 310 K
GB parameter(s) missing or negative for atom
Hello Justine:
I've got the following messages by command:
grompp -f implicit.mdp -c complex.pdb -p complex.top -o test.tpr
Setting gen_seed to 18463
Velocities were taken from a Maxwell distribution at 310 K
GB parameter(s) missing or negative for atom type 'OS'
Hi Justin:
thank you so much for such kind and helpful comments. My system is a
protein/ligand system.
I will try it with your advices these days.
best
Albert
On 10/17/2012 07:58 PM, Justin Lemkul wrote:
On 10/17/12 1:52 PM, Albert wrote:
Hi Justin:
Thank you very much for eply.
So th
On 10/17/12 1:52 PM, Albert wrote:
Hi Justin:
Thank you very much for eply.
So the modified .mdp file (including the GBSA model setting) is the following?
Is this correct?
No. See inline comments.
title = Protein-ligand complex NVT equilibration
define = -DPOSRES ; position restrain the
Hi Justin:
Thank you very much for eply.
So the modified .mdp file (including the GBSA model setting) is the
following? Is this correct?
title = Protein-ligand complex NVT equilibration
define = -DPOSRES ; position restrain the protein and ligand
; Run parameters
integrator = sd ;
nsteps = 50
On 10/17/12 1:43 PM, Albert wrote:
hello Justin:
thanks a lot for kind reply.
I've got another question: how to disable PBC? shall I simply delete "pbc=xyz"
from .mdp file? I found that sometimes if we delete some parameters from .mdp,
gromacs will use the default instead of disable it.
The
hello Justin:
thanks a lot for kind reply.
I've got another question: how to disable PBC? shall I simply delete
"pbc=xyz" from .mdp file? I found that sometimes if we delete some
parameters from .mdp, gromacs will use the default instead of disable it.
thank you very much
best
Albert
On 10/
On 10/17/12 1:35 PM, Albert wrote:
thank you all the same. I saw many people use Amber for REMD and few people use
Gromacs for REMD and the parameters is not easy reachable. However, what I found
is that Amber use cutoff=999
I am just wondering, shall I also use such big value for the followin
thank you all the same. I saw many people use Amber for REMD and few
people use Gromacs for REMD and the parameters is not easy reachable.
However, what I found is that Amber use cutoff=999
I am just wondering, shall I also use such big value for the following?
rlist = 999; short-range neighbo
I am no expert in implicit solvent simulations but I think for these
simulations it is better to use stochastic dynamic integrators with no
pbc (instead of NVT) and infinite (or very large) cut-off distances because
there is no actual water molecule in your simulation box and [normally] you
do not
Hi Saber:
thanks a lot for such kind reply.
How about the second question? I don't find any tutorial for the GBSA
solvent simulation in Gromacs website and I am not sure what kind of
parameters we should use for GBSA.
thank you very much
best
Albert
On 10/17/2012 05:48 PM, saber naderi wro
Hi Albert,
Regarding you first question, your protein is relatively big and in my
opinion 28 replicas is not much for a protein made of 290 AA with the
temperature range of 280-530. One thing that you can do is to use a lower
value for exchange probability to have less replicas. By doing this the
hello:
I am going to perform replica exchange MD with Gromacs and I found
some problems there:
1. my protein have around 290 aa with 4680 atoms. If I would like to
perform with implicite solvent with exchange probability 0.2, I found
from http://folding.bmc.uu.se/remd/ that I will have to g
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