James Starlight wrote:
Yes I've tried this way but obtained wrong result ;o
e.g after align along X I've tried rotate along Z on 90 to obtain align on Z
-rotate 0 0 90
but I've obtained structure aligned on Y :DD
Whta I've done wrong?
You've rotated around the wrong axis.
-Justin
James
2011/10/29 Mark Abraham <[email protected]
<mailto:[email protected]>>
On 29/10/2011 9:47 PM, James Starlight wrote:
sure but I could not find possible parameter for -scale option
Huh? What has scaling got to do with it?
-[no]princ bool no Orient molecule(s) along their
principal axes
from that I found that only yes\ no options is aviable for princ :(
So align with X with -princ. Then in another call to editconf rotate
it to align with whatever you want.
Mark
of course I could do the ssame via combination of the
-align vector 0 0 0 Align to target vector
-translate vector 0 0 0 Translation
-rotate vector 0 0 0 Rotation around the X, Y and Z axes in
degrees
but this would require many calculations so I'm looking for most
simplest way of orientation of my molecule along required coordinate
2011/10/29 Mark Abraham <[email protected]
<mailto:[email protected]>>
On 29/10/2011 7:38 PM, James Starlight wrote:
Mark, hello!
It's clear now about termii
also I'd like to know about orientation of my protein along
specific axis
e.g editconf -princ orient my protein along X but what should
i do to orient it along other axis?
Did you start by trying to look up the answer in editconf -h
yourself?
Mark
James
2011/10/29 Mark Abraham <[email protected]
<mailto:[email protected]>>
On 29/10/2011 6:34 PM, James Starlight wrote:
Justin, hello!
I've desided to make simulation of my GA peptide
under GROMOS96 53A6 force field extended with Berger
lipids ( on analogy to KALP simulation because both
of that lipids are membrane alpha helices with
similar topology )
About termii- As I understood you've added ACE and
NH2 termii to KALP via Amber tools software. I havent
that software now but pdb2gmx under GROMOS96 53A6
force field may add only NH(2) cap to the C-end and
COO(H) to the N-end instead of ACE and NH2.
I can't understand any of that :)
Identified residue VAL2 as a starting terminus.
Identified residue TRP16 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for VAL-2
0: NH3+
1: NH2
2: None
It's not quite unferstand for me why pdb2gmx add the
termii in such wrong manner ( e.g ACE and other
groups also contains in the .rtp of this ff).
Termini are added by pdb2gmx using the terminus databases
in the .n.tdb and .c.tdb files, as you would know from
your reading of chapter 5 of the manual :-) Only things
that are found there can be added by pdb2gmx - and not
everything you can imagine will be found there. If you
want (for example) an ACE group at your N-terminus, you
need to build it using some other tool, and arrange for
the .rtp entry for ACE to exist (which it already does).
Finally why I cant chose NH(2) for the last residue
and the COOH for the first ?
Because they've either not been parameterized, coded or
tested.
And what difference beetwen such termii specification
would be as the consequence ?
Mark
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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