On 7/19/13 10:06 AM, afsaneh maleki wrote:
Dear Justin
I copied all of files in oplsaa.ff folder in my working directory and
edited the atomname2type.n2t file as mentioned in before post in my working
directory.
I used these command:
] g_x2top –f .pdb –o .top -pbc –ff oplsaa
And gr
Dear Justin
I copied all of files in oplsaa.ff folder in my working directory and
edited the atomname2type.n2t file as mentioned in before post in my working
directory.
I used these command:
] g_x2top –f .pdb –o .top -pbc –ff oplsaa
And gromacs get me:
opening force field file
/usr/
On 7/19/13 9:32 AM, afsaneh maleki wrote:
Dear Justin
I want a topology for an arbitrary molecule (44 atom) and I use x2top
program that .n2t file is it’s input.
The .pdb file is as the following:
ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00
ATOM 2 C21 TPT 1
Dear Justin
I want a topology for an arbitrary molecule (44 atom) and I use x2top
program that .n2t file is it’s input.
The .pdb file is as the following:
ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00
ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00
ATOM
On 7/19/13 9:10 AM, afsaneh maleki wrote:
Dear Justin
thanks for your reply,
I did it. when I put the .n2t in my working directory,I have gotten this
error.
What error?
-Justin
--
==
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department o
Dear Justin
thanks for your reply,
I did it. when I put the .n2t in my working directory,I have gotten this
error.
thanks in advance,
Afsaneh
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On 7/19/13 8:53 AM, afsaneh maleki wrote:
Dear Justin
I want a topology for an arbitrary molecule (44 atom) and I use x2top
program that .n2t file is it’s input.
The .pdb file is as the following:
ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00
ATOM 2 C21 TPT
Dear Justin
I want a topology for an arbitrary molecule (44 atom) and I use x2top
program that .n2t file is it’s input.
The .pdb file is as the following:
ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00
ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00
ATOM
Zhiping Xu wrote:
> Hi all:
> I have a basic question here. I want to simulate a infinite alpha-helix
> protein, say alanine represented using a unit cell containning 11 residues.
> Now I want to simulate it in GROMACS but don't know how to generate TOP
> for the structure, i.e. the connectivity
Hi all:
I have a basic question here. I want to simulate a infinite alpha-helix
protein, say alanine represented using a unit cell containning 11 residues.
Now I want to simulate it in GROMACS but don't know how to generate TOP for the
structure, i.e. the connectivity between the 1st residue and
Tandia, Adama wrote:
Dear ALL,
I have generated from Accelrys (Materials Studio) a structure composed
of a substrate topped by a layer of organic molecules. The structure can
be saved into a .pdb format.
Is there out there a tool that I could use to generate the corresponding
topology file for
Dear ALL,
I have generated from Accelrys (Materials Studio) a structure composed
of a substrate topped by a layer of organic molecules. The structure can
be saved into a .pdb format.
Is there out there a tool that I could use to generate the corresponding
topology file for Gromacs?
Thank you in
David Mobley wrote:
All,
Is there any way to automatically generate a topology file containing
all of the parameters that normally would come from the force field?
For example, filling in each bond in the [ bonds ] section with
explicit parameters that would instead usually come from the include
All,
Is there any way to automatically generate a topology file containing
all of the parameters that normally would come from the force field?
For example, filling in each bond in the [ bonds ] section with
explicit parameters that would instead usually come from the included
force field file wh
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