[gmx-users] Parametrisation of the heteroatomic pdb
Justin A. Lemkul
jalemkul at vt.edu
Sat Oct 29 14:09:21 CEST 2011
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 <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>
>
> 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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--
========================================
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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