On 1/15/20 12:27 AM, Sundari wrote:
I tried all the options.. I load gro file instead of xtc. At zero frame I
gave representations new cartoon + secondary structure.. then I calculate
sec str details by going on vmd timeline.
I don't know what I am missing.. I am doing the same which I used al
I tried all the options.. I load gro file instead of xtc. At zero frame I
gave representations new cartoon + secondary structure.. then I calculate
sec str details by going on vmd timeline.
I don't know what I am missing.. I am doing the same which I used all the
time.
Because these are two totally
On 1/13/20 9:15 AM, Sundari wrote:
Yes, Sir, I made the gro file for a particular time by using "gmx
trjconv" command ( also checked with -pbc mol, whole, no_jump options )
but every time the 2ndary structure visualization in vmd is different from
dssp sequence of residues in gromacs. Fox ex
Yes, Sir, I made the gro file for a particular time by using "gmx
trjconv" command ( also checked with -pbc mol, whole, no_jump options )
but every time the 2ndary structure visualization in vmd is different from
dssp sequence of residues in gromacs. Fox example in my protein dssp shows
8 residue
On 1/13/20 7:22 AM, Sundari wrote:
Hello Dear,
Actually I was thinking the same i.e. gromacs use "dssp" criteria and vmd
use "stride" algorithm for secondary structure determination.
But the expected error in the two algorithms should not be more than 5%
according to the literature. Here, In
Hello Dear,
Actually I was thinking the same i.e. gromacs use "dssp" criteria and vmd
use "stride" algorithm for secondary structure determination.
But the expected error in the two algorithms should not be more than 5%
according to the literature. Here, In my case, the structure contains a lot
of
Hi,
VMD and dssp may use a slightly different criteria to define a beta
sheet.
First I will check in literature if the criteria are the same.
In some case, it occur that the the atom types (e.i H) are not properly
recognized by the software,
and thus secondary structure element can not be determ
