[gmx-users] Parametrisation of the heteroatomic pdb

[Mark Abraham]

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 <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
>
>     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 <Mark.Abraham at anu.edu.au
>>     <mailto:Mark.Abraham at anu.edu.au>>
>>
>>         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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>>
>>
>
>
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