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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