). 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
> wrote:
> > Dear all,
> > I have been trying to evaluate a paper that used amber99
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 charm
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 afte
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
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 wrote:
>
>
> On 9/12/13 7:04 PM, Rafael I. Silverman y de la Vega wrote:
>
>> I see,
>> when you say thorough parametrizatio
I see,
when you say thorough parametrization and validation, what do you mean?
How does one validate the system, calculate free energy in solution and
compare it to tabulated data?
On Wed, Sep 11, 2013 at 4:57 PM, Justin Lemkul wrote:
>
>
> On 9/11/13 6:07 PM, Rafael I. Silverman y d
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?
As long as the atom type isnt too different, t
constants the same thing?
On Tue, Sep 10, 2013 at 10:34 AM, Justin Lemkul 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, t
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.
Che
Did you follow the link in the error message?
On Wed, Sep 4, 2013 at 7:17 PM, Golshan Hejazi wrote:
> 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 steepest decent. As
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 wrote:
> It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to have
> an impact. I've tried being gentle,
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
> >> -1445435.70 0 -nan
> >> -1445435.60 0 -nan
> >> -1445435.50 0 -nan
> >> -1445435.40 0 -nan
> >> -1445435.30 0 -nan
> >> -1445435.20 0 -na
;
> flag and see how many non-finite energies do you hit. Maybe all (number of
> frames times 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
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
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 a
a text editor
On Tue, Aug 27, 2013 at 1:54 PM, The One And Only wrote:
> 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
> * Please search
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 wrote:
> So I started following some tutorials online since I didn't get a response
> last time. the tutorial I'm using i
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