[gmx-users] Parametrisation of the heteroatomic pdb

[James Starlight]

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?

James

2011/10/29 Mark Abraham <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>
>
>>  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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>
>
>
>
>
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