Hi all
I used do_dssp command to analyze structural changes of my protein.
after converting to pdf format
I realized that the Y axis of my diagram is very compress and it is not
recognizable ( residue axis) . I also change my ps.m2p file part y-major
and
y-minor.
y-major = 5.0
y-minor = 1.0
On 2/22/15 6:18 AM, nazli kashani javid wrote:
Hi all
I used do_dssp command to analyze structural changes of my protein.
after converting to pdf format
I realized that the Y axis of my diagram is very compress and it is not
recognizable ( residue axis) . I also change my ps.m2p file part
Thanks for your reply Dr. Lemkul
I changed the bond length to zero in my topology file, forcefield file and
in the n2t file. I also added the [ exclusion] section-
[ exclusions ]
; iatom excluded from interaction with i
123456 7 8
213456 7
Dear all,
I want to buy a system to run the molecular dynamics of proteins by
gromacs. Now, I have two options to buy the best system. which system
could be faster for my MD studies?
system A: COY intel xeon e1226 3.3GHz, 8mb cashe, 32gb DDR3 RAM, HDD
2TR, power 250r.
system B: Mainboard : ASUS -
Thanks
Sent from my iPhone
On Feb 22, 2015, at 5:00 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/22/15 6:18 AM, nazli kashani javid wrote:
Hi all
I used do_dssp command to analyze structural changes of my protein.
after converting to pdf format
I realized that the Y axis of my
Dear Gromacs user,
I am running mdrun to minimize (energy minimization) my structure
co-ordinate, but every time it stuck by displaying following error
Back Off! I just backed up em.log to ./#em.log.8#
Reading file em.tpr, VERSION 5.0.4 (single precision)
Using 1 MPI thread
Using 16 OpenMP
Hi every body
1- In the phosphate group, we have 4 oxygen atoms that bond to the
phosphate. Two of them are as follow: CH2-O-P-OH and the others include:
- A double bond is on the top of phosphor atom
- A OH group is at the bottom of phosphor atom
We put the atom type
