[gmx-users] Parametrisation of the heteroatomic pdb

James Starlight jmsstarlight at gmail.com
Sat Oct 29 12:47:56 CEST 2011


sure but I could not find possible parameter for -scale option

-[no]princ   bool   no      Orient molecule(s) along their principal axes

from that I found that only yes\ no options is aviable for princ :(

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>

>  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>
>
>> 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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