I think you can go for Swissviewer rather going for modeller
On Sat, 17 Dec 2016 at 12:04 PM, Seera Suryanarayana
wrote:
> Dear Justin,
>
>
>
> I apologize you as I am wasting your valuable time.
>
>
>
> I have peptide with 69 residues and some of the SER and THR residues
>
> are phosphoryla
Dear Justin,
I apologize you as I am wasting your valuable time.
I have peptide with 69 residues and some of the SER and THR residues
are phosphorylated and also some of the missing residues(1 to 6; 36 to 41
and 69) have been modeled by modeller . I have chosen charmm36 force
field.
When
I have asked this question a few days back; I try one more time:
When I am trying calculate the degrees of overlap of subsets of a
simulation to the whole trajectory by following the explanation in the
manual gmx anaeig:
"When -v, -eig, -v2 and -eig2 are given, a single number for the
overlap betw
On 12/16/16 7:46 AM, Sim gmx wrote:
Hi all,
I would like to know what you consider to be the ideal refinement for a
topology created by ATB ?
How far should we go in the manual refinement ?
For instance, ATB gave me a topology for a molecule with an unsaturated
acyl chain. Here are some poten
On 12/16/16 2:54 AM, tasneem kausar wrote:
Dear
Justin Sir
I am doing protein and drug MD simulation. I have generated the itp file of
drug from PRODRG. I have calculated the charge on the atom using HF/6- 31G*
basis set from orca3.0. Is this a right protocol to use it in GROMACS for
the charg
On 12/16/16 12:33 AM, Seera Suryanarayana wrote:
First of all I am extremely sorry for my mistake. I haven't sent you the
modified coordinate file.
I have peptide with 69 residues and some of the SER and THR residues
are phosphorylated and also some of the missing residues(1 to 6; 36 to 41
and
On 12/15/16 11:05 AM, maria khan wrote:
Dear gromacs users..
I have the following questions.
1) ::how i analyse trajectory using VMD?
Consult the VMD documentation, tutorials, and mailing list.
2)::Trajectory analysis for overall protein structure stability??
Define "overall protein str
On 12/15/16 10:15 AM, Alex wrote:
Thanks Justin for your response.
Surly PMF is better, but the point is that via FEP I have already calculate
the binding free energy of a charged amino acid to a solid surface while
Na+ used as counter-ion where both "amino acid and Na+" considered as a
single
Hi Peter,
Thanks for the reply, I know we spoke in length on this mater only just
recently. Many thanks for that.
I’ve taken the time step of collagen in vacu down to 0.0001 and I’ve
dropped the temp down to 280. I hope, running over 16 cores for two days
that this should relieve any tension in
Hi all,
I would like to know what you consider to be the ideal refinement for a
topology created by ATB ?
How far should we go in the manual refinement ?
For instance, ATB gave me a topology for a molecule with an unsaturated
acyl chain. Here are some potential issues with this topology:
1) Thre
As a note to Alex (and the rest of the list), the coarse-grained Martini
forcefield is usually run with timesteps between 20-40 fs. 15fs is
already rather low. I do agree that longer equilibration at low timestep
(5 or 10) might help.
Alternatively, Do you think a semiisotropic pressure coupling m
Dear all,
I was running my gromacs simulations on Gromacs 4.5.5 version but my system got
updated and it changed to Gromacs 5.1.2. No when I run the same energy
minimization file as earlier but just adding cutoff-scheme = Verlet, my energy
minimization is not running. Following is the message
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