Hi ,Mark:
I had announced that my system is a dimer with each peptides have 6
residues in my first post.
I'm sorry if I didn't express it to be understood easily.
Can you please tell me why 13 coils are reasonable if my systems is a dimer?
regards,
Hsin-Lin
Hi, Justin:
I post my coordinate
- Original Message -
From: Hsin-Lin Chiang
Date: Thursday, May 27, 2010 0:28
Subject: [gmx-users] Re: the output of do_dssp
To: gmx-users@gromacs.org
> Hi, Justin:
>
> I post my coordinate with protein translated by trjconv
> By this gro file, I get 0 structure and 13 coi
Hsin-Lin Chiang wrote:
Hi, Justin:
I post my coordinate with protein translated by trjconv
By this gro file, I get 0 structure and 13 coils.
Analyze both chains separately using index groups. I would also encourage you
to file a bugzilla about this issue. If you consider residues 1-6 and
Hi, Justin:
I post my coordinate with protein translated by trjconv
By this gro file, I get 0 structure and 13 coils.
regards,
Hsin-Lin
Generated by trjconv : Protein in water t= 0.0
144
1LEU N1 2.499 1.707 2.735 -0.1664 0.1749 0.5034
1LEU H12 2.496 1
Hsin-Lin wrote:
Hi, Justin
Thank you for your patience.
According your reply, I used trjconv to write only protein group into another
file.
I execute do_dssp again in group “protein”and “mainchain” respectively but
still get coils more than total residues.
Can you post the text of your
Hi, Justin
Thank you for your patience.
According your reply, I used trjconv to write only protein group into
another file.
I execute do_dssp again in group "protein"and "mainchain" respectively but
still get coils more than total residues.
Why?
Hsin-Lin
Hsin-Lin wrote:
> Hi, Justin:
>
> T
Hsin-Lin wrote:
Hi, Justin:
Thank you for your reply.
I try to select the group, 'mainchain', when prompted, and get the quantity
of coil still larger than the number of residues of my protein.
Then some other elements of your system are being detected as containing
relevant atoms. What ha
Hi, Justin:
Thank you for your reply.
I try to select the group, 'mainchain', when prompted, and get the quantity
of coil still larger than the number of residues of my protein.
The data is the same as the output that generated by the selection, "1.
Protein".
If I select backbone, I get the fatal
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