Hi, Thomas!
I'd like to ask you some addition questions about FMA. As I understood
from the FMA page that technique is something like integrator of
principal components (merge some PCs with identical functional motion
seen in the X-ray structures for instance) calculated from g_covar. So
FMA is al
Probably remove the overlapping lipid then. Once you run MD it will repack.
On 2012-12-15 09:19:49PM -0800, Shima Arasteh wrote:
> Thanks for your kind reply.
> My system is composed of protein packed by lipids. The atoms overlapping, are
> protein ( atom 288) and lipid chain. I think if I move
Dear Dr. Shirts!
Could you tell me is there any difference of different Tau_t ussage (
inverse friction in case of Stochastic dynamics) for simulation of
water-soluble as well as membrane-proteins ? In the first case I'm
using tau_t 2ps that is lower than internal water friction. In the
second ca
Dear collegues!
Oppositely to the Bipin Singh's question I wounder to know about the
exploring ( radius expansion) mode of EDS. For example I define
essential
subspace from some collective coordinates and then run MD in that
subspace in exploring mode of EDS. Will the system be biased to the
some
Justin,
It's not quite understood for me why such errors occurs in the atoms
of standard residues when I've bounded them to the C term of my
chromophore if the geometry of the adjacent residues might not be
changed. So it likely that some errors occur during parametrization of
the molecule which I
Thanks for your kind reply.
My system is composed of protein packed by lipids. The atoms overlapping, are
protein ( atom 288) and lipid chain. I think if I move them, I may get some
other clashes, may I not?
Any other suggestion?
Thanks.
Sincerely,
Shima
- Original Message -
From
It depends on what the atom is overlapping with and some conjecture as to
what might be causing the overlap:
You can always manually move it, either by editing the .gro file directly
or using a tool like VMD to move it or the molecule/fragment it's attached to
with the mouse and then display the
When I find overlapping atom, what should I have to do? How is it possible to
get solved?
Would you please help me?
Sincerely,
Shima
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Saturday, September 29, 2012 3:01 PM
Subj
Hi fatemeh,
I am looking for prameters like yours, where have you took the parameters
for gold and gold-aminoacid inteaction?
Francesco
2012/12/16 Peter C. Lai
> Where is the .itp file for the system?
>
> On 2012-12-15 01:40:27PM -0800, fatemeh ramezani wrote:
> > hi
> >
> >
> > I'm simulating
Where is the .itp file for the system?
On 2012-12-15 01:40:27PM -0800, fatemeh ramezani wrote:
> hi
>
>
> I'm simulating gold atom interaction with aminoacidcys. I have made
> gold-cys.pdb by hyperchem software:
>
> HETATM 1 N CYS 1 0.000 1.335 0.000
> HETATM 2 CA CY
hi
I'm simulating gold atom interaction with aminoacidcys. I have made
gold-cys.pdb by hyperchem software:
HETATM 1 N CYS 1 0.000 1.335 0.000
HETATM 2 CA CYS 1 -0.683 1.818 -1.183
HETATM 3 C CYS 1 -0.705 3.339 -1.221
HETATM 4 O CYS
On 12/15/12 2:18 PM, James Starlight wrote:
So as I understood it've happened because the conformation of the
adjacent residue is differ when that residue bounded to the
chromophore ( in comparison to the residue in unbound capped form).
Conformation is irrelevant; atom types are all that ma
So as I understood it've happened because the conformation of the
adjacent residue is differ when that residue bounded to the
chromophore ( in comparison to the residue in unbound capped form).
But in term of the backbone geometry of C and N-terms chromophore is
like a typical amino acid. Also Chr
On 12/15/12 4:03 AM, mirc...@sjtu.edu.cn wrote:
Dear All:
I encountered a problem when doing umbrella sampling. The distance calculated
by grompp and g_dist is different, as shown by the following:
grompp z component of g_dist(since I am constraining the distance between two
groups along t
On 12/15/12 10:58 AM, John Doe wrote:
Hello All,
I was wondering if it's possible to print to a file different thermo data, such
as force on atoms, pressure, bond energies, ect?
Energy terms are stored in the .edr file and forces on atoms are stored in the
.trr file provided you set nstf
On 12/15/12 1:34 PM, James Starlight wrote:
The last problem with which I've forced during preparation of my
chromophore is when I've defined bond between chromophore and the next
residue
C+N
That produce 15 addition errors about unknown UB and dihedral types
in the atoms of the next res
On 12/14/12 11:42 PM, James Starlight wrote:
The topology with the below params produced that 118 errors during
grompp processings ( after pdb2gmx processing the geoetry of the
mollecule was correct )
[CRN]
[ atoms ]
CG2 CA-0.0900 0
CD1 CA-0.0800 1
CD2 CA-0.0800 2
CE1 CA-
The last problem with which I've forced during preparation of my
chromophore is when I've defined bond between chromophore and the next
residue
C+N
That produce 15 addition errors about unknown UB and dihedral types
in the atoms of the next residue (not in the chromophore) where all UB
and i
Hello All,
I was wondering if it's possible to print to a file different thermo data, such
as force on atoms, pressure, bond energies, ect?
Thanks
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http://lists.gromacs.org/mailman/listinfo/gmx-users
* P
Dear All:
I encountered a problem when doing umbrella sampling. The distance calculated
by grompp and g_dist is different, as shown by the following:
grompp z component of g_dist(since I am constraining the distance between two
groups along the z direction, I should calculate the z component o
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