On Mon, Jun 11, 2012 at 11:08 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Maybe you could use ptraj to center the solute in the box?
>
> Bill
That is a good suggestion, however also the cloud of counterions
should accompany the protein-complex. Don't know how to do that.
Actually, MD is going on without any problem: protein-complex and
counterions remain inside the water box, albeit not at the center. I
assume that there should be nothing wrong in continuing this way (I
would like to see if the ligand adapts to the enzyme active center; so
far it is going this way).
thanks
francesco pietra
>
> Francesco Pietra <chiendarret.gmail.com> wrote:
>
>> Hi:
>>
>> Having solved (thanks to addIonsRand) the problem of setting
>> homogeneously a high number of single-charge ions around the protein
>> in a water box, I am now trying to have the protein placed with its
>> center of mass at the center of the box, which was not the case with
>> ambertools12 LEaP.
>>
>> I wonder whether there is a way to intervene manually on the prmtop
>> file. I am only aware about
>>
>> %FLAG BOX_DIMENSIONS
>> %FORMAT(5E16.8) OLDBETA, BOX(1), BOX(2), BOX(3)
>> OLDBETA : periodic box, angle between the XY and YZ planes in
>> degrees. This is now redundant, as it is present in the
>> inpcrd files. It is ignored here.
>> BOX : the periodic box lengths in the X, Y, and Z directions.
>> This is now redundant, as it is present in the inpcrd files.
>> It is ignored here.
>>
>> The following are only present if IFCAP .gt. 0
>>
>> %FLAG CAP_INFO
>> %FORMAT(10I8) NATCAP
>> NATCAP : last atom before the start of the cap of waters
>> placed by edit
>>
>> %FLAG CAP_INFO2
>> %FORMAT(5E16.8) CUTCAP, XCAP, YCAP, ZCAP
>> CUTCAP : the distance from the center of the cap to the outside
>> XCAP : X coordinate for the center of the cap
>> YCAP : Y coordinate for the center of the cap
>> ZCAP : Z coordinate for the center of the cap
>>
>> The "5E16.8" section is indeed present in my prmtop file, however
>> clearly not manageable. Is any raw information about the center of
>> mass of the protein relatively to the center of the box, on which to
>> intervene?
>>
>> What is wrong in my pdb fine, so that the result of "5E16.8" is
>> misplacing the protein into the water box, defeated my understanding.
>>
>> Thanks
>> francesco pietra
>>
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Received on Tue Jun 12 2012 - 02:30:02 PDT
