Dear all,
I have been trying to evaluate a paper that used amber99 with SPC water to
simulate a protein. How would this affect the results, is it important? I
googled for a bit, all I found was:
Amber, charmm and OPLS-AA were developed with TIP3P, and that should be
the default. Except that
were seen). If the
paper does not support its decision to mix and match, go and ask them
why it was reasonable!
Mark
On Tue, Sep 24, 2013 at 10:58 PM, Rafael I. Silverman y de la Vega
rsilv...@ucsc.edu wrote:
Dear all,
I have been trying to evaluate a paper that used amber99 with SPC water
:
On 9/17/13 8:18 PM, Rafael I. Silverman y de la Vega wrote:
Can you give some examples of how these verifications are different for
different force fields? It doesnt seem like verifying takes that much
time,
but a theorist prof in my department told me not to worry as long as my
system doesnt
Sulpher is important, but it is in the apoprotein, not the parametrized
prosthetic group
On Thu, Sep 19, 2013 at 6:51 PM, Rafael I. Silverman y de la Vega
rsilv...@ucsc.edu wrote:
Hmm, I will have to do some more controls then, but I prob dont have time
to do them till after quals this fall
into the delta positive hydrogen on the same phosphate. Is that thorough in
your opinion?
Thanks
On Thu, Sep 12, 2013 at 7:32 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/12/13 7:04 PM, Rafael I. Silverman y de la Vega wrote:
I see,
when you say thorough parametrization and validation, what do
y de la Vega wrote:
Hi all,
in another thread it was recommended that instead of changing the atom
types by analogy to ones with the desired parameter already assigned, that
instead one should assign bonded parameters by analogy. I was just
wondering how this is better?
I didn't suggest
Adding parameters can be a little bit of a pain, you could instead change
the atom types in the molecule parameter, to ones that have defined angles
and bond types with each other. Of course, you would need to make sure that
you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc.
constants the same thing?
On Tue, Sep 10, 2013 at 10:34 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote:
Adding parameters can be a little bit of a pain, you could instead change
the atom types in the molecule parameter, to ones that have
Did you follow the link in the error message?
On Wed, Sep 4, 2013 at 7:17 PM, Golshan Hejazi golshan.hej...@yahoo.comwrote:
Hi everyone,
I am simulating a system of paracetamol crystal in ethanol solvent. I used
pdb2gmx to generate the topology and gro file and I minimized the system
using
Have you tried with even less restraints? I found systems are not always
stable with more than the bare minimum of restraints
On Sun, Sep 1, 2013 at 7:54 PM, Trayder Thomas trayder.tho...@monash.eduwrote:
It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to have
an impact.
Hi all,
I am trying to insert a water into a prosthetic group binding cavity. I
cant seem to get an output .pdb file of the insertions, I set GMX_TPI_DUMP
in my shell with $ export GMX_TPI_DUMP=xxx but no numbers seemed to work. I
cant really get good information out of the .xvg output either, it
Thanks for the reply João,
I am using gromacs 4.6.3, I did centre all 4 frames at the prosthetic
group.
I tried GMX_TPI_DUMP = 5.0e+3, 5.0e+20, and even 5.0e-03, still, not a
single .pdb file written.
I am doing this on a 4 frame trajectory, consisting of ~7000 atoms per
frame. I think it may have
the number of insertions?
Can you post 100 lines or so of your .xvg file? I'm curious about it. Maybe
4.6.3 has some new output I'm unaware of.
Also, can you tell something more about your system?
Best,
João
On Sat, Aug 31, 2013 at 12:55 AM, Rafael I. Silverman y de la Vega
rsilv
it as the last
coordinate on the .tpr file you're building, see the manual). In short:
be
careful with your trjconv command and maintain the integrity of the
trajectory (PBC, wholeness, for example).
Best,
João
On Sat, Aug 31, 2013 at 1:30 AM, Rafael I. Silverman y de la Vega
Thanks!
I will try these latest suggestions!
On Fri, Aug 30, 2013 at 7:27 PM, Rafael I. Silverman y de la Vega
rsilv...@ucsc.edu wrote:
Yes, I hand edited the .tpr file to get the thing to work, otherwise I got
errors with particle numbers being different.
On Fri, Aug 30, 2013 at 6:54 PM
a text editor
On Tue, Aug 27, 2013 at 1:54 PM, The One And Only chappybo...@gmail.comwrote:
What kind of editor should I open it in? I have Pymol, but I don't know if
it's the right one.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
It sounds like you dont have the .pdb file in your working directory.
Perhaps you need to learn a bit about unix filesystems
On Sat, Aug 24, 2013 at 6:18 PM, The One And Only chappybo...@gmail.comwrote:
So I started following some tutorials online since I didn't get a response
last time. the
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