Dear users,
I wanna pack the lipids around my protein. To do so, InflateGro methodology is
applied. Following Justin's tutorial KALP15-DPPC, the first step is scaling up
4 times:
# perl inflategro.pl system.gro 4 POPC 14 system-inflated.gro 5 area.dat
and then shrinking it for 26 times.
I'd
Why don't you just try it and see what happens?
On 2012-09-23 12:19:20AM -0700, Shima Arasteh wrote:
>
>
> Dear users,
>
> I wanna pack the lipids around my protein. To do so, InflateGro methodology
> is applied. Following Justin's tutorial KALP15-DPPC, the first step is
> scaling up 4 times:
I don't know! :))
Sincerely,
Shima
- Original Message -
From: Peter C. Lai
To: Discussion list for GROMACS users
Cc:
Sent: Sunday, September 23, 2012 10:52 AM
Subject: Re: [gmx-users] InflateGro methodology
Why don't you just try it and see what happens?
On 2012-09-23 12:19:20AM
Dear Gromacs users
i am doing NPT Eqlibration for a cyclic
peptide
When I run grompp I have got Warning as follows
WARNING 1 [file 2KDQ3.top, line 1137]:
The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H has
an estimated oscillation
On 9/23/12 1:31 AM, Ali Alizadeh wrote:
Dear All users
When run grompp program for my system, I encounter this error:
grompp -f grompp.mdp -c hyd1.gro -p hyd.top -o hyd.tpr
Fatal error:
Atomtype K not found
But i have not atomtype K in my input files,
Apparently you do. Check more clos
On 9/23/12 4:17 AM, vidhya sankar wrote:
Dear Gromacs users
i am doing NPT Eqlibration for a cyclic
peptide
When I run grompp I have got Warning as follows
WARNING 1 [file 2KDQ3.top, line 1137]:
The bond in molecule-type Protein_chain_A between ato
I presume you are referring to Essential Dynamics Sampling, described in
section 3.14 of the manual (v4.5.4). There is also a great tool that finds
the few PCs that are maximally correlated to a functional quantity (e.g.
the volume of the active site). The technique is coined Functional Mode
Analys
On 21/09/2012 11:08 PM, Bastien Loubet wrote:
Justin Lemkul wrote
On 9/21/12 8:29 AM, Bastien Loubet wrote:
Dear gmx users,
We recently got a problem with the rerun feature of mdrun, and we request
your help in order to help to solve it.
We have run a simulation of a large POPC membrane using
Thomas,
thank you for the explanation
1) Indeed ED sampling was exactly that I need. It's not quite
understand for me about correct chose of that parameters for biassing
simulation
-linfix string Indices of eigenvectors for fixed increment
linear sampling
On 23 September 2012 17:18, James Starlight wrote:
> Thomas,
>
> thank you for the explanation
>
> 1) Indeed ED sampling was exactly that I need. It's not quite
> understand for me about correct chose of that parameters for biassing
> simulation
>
> -linfix string Indices of eigenvec
Thomas,
thanks again for explanation. Its also intresting to me is it possible
to do further biassed MD guided on that FMA modes as well as obtain
projections onto that FMA sub-spaces of X-ray datasets for instance ?
( e.g for comparison of the results from FMA of experimental data as
well as MD_d
Please keep the discussion on the list.
On 9/23/12 11:45 AM, Asaf Farhi wrote:
Dear Justin
Thank you very much for the reply.
I apologize that I take of your time.
I need this file in order to demonstrate a method for free energy calculation
that I'm working on (using Matlab).
I don't have Gr
Dear Justin
Thank you very much for the reply.
I apologize that I take of your time.
I need this file in order to demonstrate a method for free energy calculation
(using Matlab).
I don't have Gromacs installed. If you can, and it's legal I would be happy to
have such a file so I can use
realist
Hi,
I would first do an alignment between the two proteins and then do PCA
using only the Ca atom coordinates of the common atoms (or the ones you
think are equivalent). I would also remove the very flexible loops to
extract pure low-frequency motions with PCA. At the end you must have two
eigensp
Justin, Francesco,
thanks for advises.
James
2012/9/21 Justin Lemkul :
>
>
> On 9/21/12 2:11 AM, James Starlight wrote:
>>
>> Dear collegues
>>
>> Thank for advices. Indeed Gromacs is able to analyse two trajectories
>> with g_rms ( with the flags -f and -f2 ) but as the result I've obtain
>> gr
Hi,
So the commands from the beginning are appended below:
pdb2gmx -vsite h -f 3HQN_tet_nolig.pdb -o system.gro
(I choose option 6 for AMBER99sb-ILDN force field and then option 2
for TIP4P water model)
editconf -f system.gro -o system_box.gro -c -d 1.0 -bt dodecahedron
genbox -cp system_box.g
On 9/23/12 2:28 PM, Ankita naithani wrote:
Hi,
So the commands from the beginning are appended below:
pdb2gmx -vsite h -f 3HQN_tet_nolig.pdb -o system.gro
(I choose option 6 for AMBER99sb-ILDN force field and then option 2
for TIP4P water model)
editconf -f system.gro -o system_box.gro -c -
Hi,
thanks again for explanation. Its also intresting to me is it possible
> to do further biassed MD guided on that FMA modes as well as obtain
> projections onto that FMA sub-spaces of X-ray datasets for instance ?
> ( e.g for comparison of the results from FMA of experimental data as
> well as
On 23/09/2012 5:22 PM, mohan maruthi sena wrote:
Hi all,
I want to do normal mode analysis for a protein using elastic
network model containing 691 residues. I consider only c-alpha atoms
connected by a spring constant of 81600 kj/nm2. When I do normal mode
analysis I get the foll
Dear all,
I have created a .GRO file from a PDB file for a polymer. However in the PDB I
have positive and negative charges of some ions where as in the produced GRO
file these disappear. Are those charged atoms taken into account in the gro
file as I will be doing a MD simulation of such poly
On Mon, Sep 24, 2012 at 12:56 PM, Elie M wrote:
>
> Dear all,
> I have created a .GRO file from a PDB file for a polymer. However in the
> PDB I have positive and negative charges of some ions where as in the
> produced GRO file these disappear. Are those charged atoms taken into
> account in th
Thanks for your help.
Elie
> Date: Mon, 24 Sep 2012 13:05:14 +0800
> Subject: Re: [gmx-users] Missing charges in a .gro file
> From: terrence...@gmail.com
> To: gmx-users@gromacs.org
>
> On Mon, Sep 24, 2012 at 12:56 PM, Elie M wrote:
>
> >
> > Dear all,
> > I have created a .GRO file from a
I've tried to make PCA from my X-ray data and forced with many problems :)
Firstly I've made pdb trajectory in NMR-like format ( by means of
pymol) consisted of all X-ray structures.
than I've make .tpr file (From the tpr of the same protein which I've
simulated previously) for the subset of C-al
Dear all,
I've done some REMD simulations using a quite high exchange attempt
frequency (10 attempts per ps) as proposed by Sindhikara et al.
("Exchange Often and Properly in Replica Exchange Molecular Dynamics",J.
Chem. Theory Comput. 2010, 6, 2804–2808 ).
Unfortunately, I have now recognized
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