AMBER Archive (2002)

Subject: Re: solvating a protein with large cavity

From: M. L. Dodson (bdodson_at_scms.utmb.EDU)
Date: Sat Dec 14 2002 - 10:23:15 CST

Maybe solvateShell is what you want?
Bud Dodson

On 14 Dec, Tom Bishop wrote:
> Dear amber,
> I'm trying to solvate a protein w/ a large cavity (~500A^3) using tleap
> in amber7.
> Since a single water is about 30A^3 large I would expect somewhere
> between 15-20 waters to be located in the cavity.
> Simply using solvatebox does not put any waters in the cavity, but fills
> up a box as one would normally expect.
>
>
> Here's the tleap input.
>
> source leaprc.ff99
> REC = loadpdb pro.pdb
> solvatebox REC WATBOX216 6
> set default OldPrmTopFormat on
> saveAmberParm REC vmd.top tmp.crd
> set default OldPrmTopFormat off
> saveAmberParm REC rec-wat.top rec-wat.crd
> savepdb REC amberout.pdb
> quit
>
> tleap does not report any errors, missing atoms, problems etc....It adds
> a bunch of water and
> looking at the output I see there is a box of water added to the system,
> but the cavity is empty!
> tleap output is attached below at the end
>
> I then tried to use solvatecap. First I identified the amino acids which
> make up the "boundary" of the cavity, assuming
> the geometric center of these a.a. would be a good estimate of position
> of the cavity, but solvatecap is apparently not determining the center
> of geometry for these selected a.a. as the manual says it should. This
> may be a syntax problem on my part, but
> I looked thru the manual to find out what a "container" is and didn't
> see anything.
>
> Here is the tleap input
> source leaprc.ff99
> REC = loadpdb pro.pdb
> CAPRES = { REC.39 REC.42 REC.45 REC.73}
> ## only a partial list of a.a. is given here b/c the actual list is very
> long
> ## just to see how things are working
> desc CAPRES
> ## all looks OK
> center CAPRES
> ## gives {0,0,0} apparently CAPRES is not a valid arguement to center.
> ## so let's not use it for solvatecap either :-)
> solvatecap REC WATBOX216 { REC.39 REC.42 REC.45 REC.73} 6
> set default OldPrmTopFormat on
> saveAmberParm REC vmd.top tmp.crd
> set default OldPrmTopFormat off
> saveAmberParm REC rec-wat.top rec-wat.crd
> savepdb REC amberout.pdb
> quit
>
> Amber does succesfully add some water to this system, but it's a small
> ball of water with radius 6A located at the origin.
> That would be fine if the center of the cavity were at the origin, but
> the 6A ball of water is not touching the protein
> since the center of mass of the protein is located about 15A from the
> origin for the coordinate set that I"m using.
>
> Any suggestions on how to fill this cavity in the protein?
> Any suggestions on how to call solvatecap with a list of residues would
> be greatly appreciated even if doesn't apply to this particular problem.
>
> Thanks,
> TOm
>
> leap.log contents, partial listing only
>
> Sequence:
> Sequence: TP3
>> solvatebox REC WATBOX216 6
> Solute vdw bounding box: 67.175 59.247 50.375
> Total bounding box for atom centers: 79.175 71.247 62.375
> Solvent unit box: 18.774 18.774 18.774
> The number of boxes: x= 5 y= 4 z= 4
> Adding box at: x=0 y=0 z=0
> Center of solvent box is: 37.548698, 28.161524, 28.161524
> Adding box at: x=0 y=0 z=1
> Center of solvent box is: 37.548698, 28.161524, 9.387175
> Adding box at: x=0 y=0 z=2
> Center of solvent box is: 37.548698, 28.161524, -9.387175
> Adding box at: x=0 y=0 z=3
> Center of solvent box is: 37.548698, 28.161524, -28.161524
> Adding box at: x=0 y=1 z=0
> Center of solvent box is: 37.548698, 9.387175, 28.161524
> Adding box at: x=0 y=1 z=1
> Center of solvent box is: 37.548698, 9.387175, 9.387175
> etc...
> etc..
> etc..
> Center of solvent box is: -37.548698, -28.161524, -9.387175
> Adding box at: x=4 y=3 z=3
> Center of solvent box is: -37.548698, -28.161524, -28.161524
> Total vdw box size: 82.086 74.160 65.657 angstroms.
> Volume: 399688.851 A^3
> Total mass 191580.364 amu, Density 0.796 g/cc
> Added 9087 residues.
>> set default OldPrmTopFormat on
>> saveAmberParm REC vmd.top tmp.crd
>
>
> and for the solvate cap part of things
>
>> solvatecap REC WATBOX216 { REC.39 REC.42 } 6
> The number of boxes: x= 1 y= 1 z= 1
> Adding box at: x=0 y=0 z=0
> Center of solvent box is: 0.000000, 0.000000, 0.000000
> Added 23 residues.
>> set default OldPrmTopFormat on
>> saveAmberParm REC vmd.top tmp.crd
>
> 

-- 
M. L. Dodson                                bdodson_at_scms.utmb.edu
409-772-2178                                FAX: 409-772-1790