Hi,
I am trying to use g_confrms to compare my initial and final structure
and fit them on their backbone. However, I notice a difference of 10
atoms in both of these structures and so I am unable to use g_confrms.
Can anyone please help me and advice me regarding this as the manual
does mention
On 16/09/2012 11:49 PM, Ankita naithani wrote:
Hi,
I am trying to use g_confrms to compare my initial and final structure
and fit them on their backbone. However, I notice a difference of 10
atoms in both of these structures and so I am unable to use g_confrms.
Can anyone please help me and
Hi Mark,
I haven't been able to figure out the reason of the difference between
the two structures. When I prompt for my backbone to be fitted against
each other, the initial structure has 2965 elements and the final
output file has 2955 elements. Could you please suggest the possible
reason for
On 17/09/2012 12:10 AM, Ankita naithani wrote:
Hi Mark,
I haven't been able to figure out the reason of the difference between
the two structures. When I prompt for my backbone to be fitted against
each other, the initial structure has 2965 elements and the final
output file has 2955 elements.
I recommend use the double precision just to check the better result to
your system. In my case, i've got much better results using emtol=0.004 and
double precision. My system is too much unstable and i tried. I have no
regrets...
Marcelo Depolo
Em 15/09/2012 22:11, Elie M
Dear all,
To simulate a lipid-protein system, I'm using CHARMM36 FF and popc lipid
bilayer. So I need to put popc.pdb, popc.itp and lipid.itp files in my working
directory. I'm wondering:
1.if it is correct to use popc.itp generated from 50 ns-simulated popc in
water?
2. I need to have
On 9/16/12 12:34 PM, Shima Arasteh wrote:
Dear all,
To simulate a lipid-protein system, I'm using CHARMM36 FF and popc lipid
bilayer. So I need to put popc.pdb, popc.itp and lipid.itp files in my working
directory. I'm wondering:
1.if it is correct to use popc.itp generated from 50
Thanks.
Yes, I want to use the coordinate file from 50-ns simulation. Would you please
let me know what the criterion for knowing that the equilibrated system is
proper for insertion of protein? Do the temperature, RMSD, pressure and
visualization of popc-water system make me decide that it
On 9/16/12 12:48 PM, Shima Arasteh wrote:
Thanks.
Yes, I want to use the coordinate file from 50-ns simulation. Would you please
let me know what the criterion for knowing that the equilibrated system is
proper for insertion of protein? Do the temperature, RMSD, pressure and
visualization
Dear Mark ,
Again Thanks for you reply
After Editing my pdb file from intial FL to FLF format
Then i Run pdb2gmx for my linaer pdb file , i have selected none for both
termini ( with -ter option) as you mailed me in the previous mail
I have got error as
On 17/09/2012 2:55 AM, vidhya sankar wrote:
Dear Mark ,
AgainThanks for you reply
After Editing my pdb file from intial FL to FLF format
Then i Run pdb2gmx for my linaerpdb file , i have selected none for both
termini ( with -ter option) as you mailed
Dear Mark,
Thank you for your reply
I have used the peptide FLF
For that pdb2gmx construct topology successfully with -ter choosing any
thing for both terminal.
But When i Choose none with -ter for both terminal It again shows error as
follows
Fatal error:
There
Hi,
I'm preparing my mdp and topology files for running free energy calculations
using BAR method. I´m using Justin Lemkul's tutorial as a reference (You can
find it here
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html).
According to this
Hi all,
I am studying a system which consists of DNA duplex 20 base pairs. Actually
I am interested in studying the base flipping of the thymine.
I have the crystal structure of extrahelical DNA in which thymine is out
side the helical structure. I want use pulling simulations to bring this
base
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