More detaily:
firstly I've parametrized my chromophore (this pdb consisted of ALL
hydrohens included for first N and last C atoms) represented as the amino
acid
antechamber -i crq.mol2 -fi mol2 -o crq2.mol2 -fo mol2 -c bcc -s 2
parmchk -i crq.mol2 -f mol2 -o crq.frcmod
than I've made lib file using
source leaprc.ff99SB
source leaprc.gaff
crq = loadmol2 crq2.mol2
loadamberparams crq.frcmod
set crq head crq.1.N
set crq tail crq.1.C
saveoff LIG ligand.lib
doe such parametrization of non-standard residue correct in general?
2014-05-14 14:15 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> In general case following to the amber's "Simulating a Solvated Protein
> that Contains Non-Standard Residues" tutorial I've found that I should
> initially create prmtop for the isolated non-standart residue firstly. How
> It could be done in my case assuming that I have pdb of my chromophore with
> added hydrogens (excluding hydrogens for first C and last N atoms which
> will be connected to the rest of the backbone)?
>
>
> *James*
>
>
> 2014-05-14 13:12 GMT+04:00 Mark Williamson <mjw.mjw.name>:
>
> On 14/05/14 09:44, James Starlight wrote:
>>
>> > Question regarding intal system preparation: for instance I have pdb
>> > consisted of GFP with chromophore and I'd like to perform qm_mm
>> simulation
>> > of this protein treating chromophore by semi-empirical approximation and
>> > rest of the protein (+ solvent) using mm. How I should prepare initial
>> > prmtop of my GFP using tleap if I lack for the parameters for
>> chromophore
>> > (wich are actualy will not be usefull during my qm-mm run) ?
>>
>> With reference to GFP chromophore parameters, the supporting information
>> in this paper *may* be of use:
>>
>> "Analytical Harmonic Vibrational Frequencies for the Green Fluorescent
>> Protein Computed with ONIOM: Chromophore Mode Character and Its Response
>> to Environment"
>>
>> http://dx.doi.org/10.1021/ct400664p
>>
>>
>> Regards,
>>
>> Mark
>>
>> --
>> Mark J. Williamson
>> Unilever Centre for Molecular Informatics
>> Department of Chemistry
>> Lensfield Road
>> Cambridge CB2 1EW
>>
>> http://www-ucc.ch.cam.ac.uk/members/mw529
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed May 14 2014 - 04:30:03 PDT
