Previous Thread
Next Thread
Print Thread
CRYST setup with solvation water: Image centering?
#17137 02/21/08 02:27 PM
Joined: Aug 2005
Posts: 26
D
drn Offline OP
Forum Member
OP Offline
Forum Member
D
Joined: Aug 2005
Posts: 26
Dear all,

I have a protein crystal (space group P6_5) with large water channels which I have set up using the CRYST commands. I believe I have eliminated all problems to do with coordinate alignment etc. (output PDB file with images look fine), and now wish to do some dynamics.

The problem is that during dynamics, water molecules leave the central asymmetric unit and the simulation crashes. In the past, I have always used various IMAGE centering commands (without the CRYST commands), but I was of the understanding that the CRYST commands should take care of this. However it seems to be BYSEG rather than BYRES, which is fine for small crystals (like the Ala example files), but not when many (mobile) water molecules are present.

Using additional IMAGE commands (IMAGE BYRES XCEN .. YCEN .. ZCEN .. SELE ( SEGID WAT ) END) doesn't seem to solve the problem. I'm just doing NVE dynamics at the moment, and am using 'IMGFRQ 10 INBFRQ -1'.

Any help, suggestions or comments would be very useful!
David.

Re: CRYST setup with solvation water: Image centering?
drn #17138 02/21/08 07:34 PM
Joined: Sep 2003
Posts: 8,506
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,506
CRYSTal provides a convenient way to set up complicated image transformations, but the user must still specify how image centering should occur. The default is to center around 0,0,0 which may be a problem in your case. It may also be a problem if the asymmetric unit was moved to be at the center.

IMAGE BYRES should work fine for water, where each molecule is a residue, given the appropriate center.

Re: CRYST setup with solvation water: Image centering?
rmv #17139 03/14/08 10:44 AM
Joined: Aug 2005
Posts: 26
D
drn Offline OP
Forum Member
OP Offline
Forum Member
D
Joined: Aug 2005
Posts: 26
Dear all,

Still having some problems with my hexagonal unit cell... I've now sorted out my image centering and a few other small errors in my setup, but there's still an odd feature which is worrying me.

The hexagonal unit cell has sides of length A and C. My water box (asymmetric unit) is a diamond shape, long diagonal A, short diagonal A/sqrt(3) and height C/2. I've got the appropriate number of water molecules in the box for the correct density. On minimisation and equilibration (NVE at the moment), the sides of the box bulge out in a symmetric way, approximately 1/3 up the height on two opposite sides, and 2/3 up the box height on the other two sides. The top and bottom of the box are flat and parallel, as they should be.

The positions of the bulges did make me think that something might be wrong with the C spacing, but I've checked this. Also, printing out a pdb with images shows no overlapping parts, nor gaps along A or C. This 'additional volume' is also a problem, since water is moving away from the sharp point of the asymmetric unit, meaning there is a 'hole' in the water.

I could perhaps solve this by generating the whole unit cell, but I want to avoid having to simulate 24 proteins and all the water if I can.

Here are some pieces of input to do with the crystal, which work fine when applied to the protein part of the crystal -- ie the lattice looks fine:
----
SET A 128.24
SET C 68.32
SET ALPHA 90
SET GAMMA 120

CALC 2RT2 = 2 * SQRT ( 2 )
CALC DIAG = @A / @2RT2
----
CRYST BUILD CUTOFF 20.0 NOPER 5
(-Y,X-Y,Z+4/6)
(-X+Y,-X,Z+2/6)
(-X,-Y,Z+3/6)
(Y,-X+Y,Z+1/6)
(X-Y,X,Z+5/6)
----
CRYST DEFINE HEXAG @A @A @C @ALPHA @ALPHA @GAMMA
----
IMAGE BYRES XCEN @DIAG YCEN @DIAG ZCEN 0.0 SELE SEGID SOL1 END
----

There's no change in going from c31b2 to c34b1 (just in case of a bug).

I attach a pdb of the water asymmetric unit which illustrates the problem.

Any suggestions?!

Attached Files
17459-equil250_1.pdb (0 Bytes, 179 downloads)
Re: CRYST setup with solvation water: Image centering?
drn #17140 03/21/08 12:53 AM
Joined: Jan 2008
Posts: 12
S
Forum Member
Offline
Forum Member
S
Joined: Jan 2008
Posts: 12
Hi!
just curious about how to print out the pdb file with primary structure and images around. You've mentioned in you post that you did it -
could you please tell the way how to do it?

Thanks!

Re: CRYST setup with solvation water: Image centering?
Stepan2 #17141 03/24/08 02:51 PM
Joined: Nov 2003
Posts: 36
Forum Member
Offline
Forum Member
Joined: Nov 2003
Posts: 36
Add the IMAG keyword to your WRIT COOR ... command line.

See io.doc for more options.


Joshua Ward Graduate Student Purdue University Department of Medicinal Chemistry and Pharmacology

Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.011s Queries: 25 (0.006s) Memory: 0.9245 MB (Peak: 1.0178 MB) Data Comp: Off Server Time: 2020-10-29 08:03:52 UTC
Valid HTML 5 and Valid CSS