AMBER Archive (2005)

Subject: AMBER: Cyclohexane solvent Box

From: chaiann ng (andy810915_at_hotmail.com)
Date: Sun Oct 16 2005 - 23:43:21 CDT


Dear Amber User,

Does anyone has cyclohexane solvent box available?
I try to build one, I have the final md.rst but I could not build the
periodic box by following David's advice, which shown below:

"Use ambpdb to convert the coordinates to pdb format, then read it back into
LEap and use the setBox command to make it periodic. Save it as on off file.
"

I output the .rst to pdb file, but the cyclohexane molecule is disperse. If
i read back into Leap, this is what happen. I have 117 residues. It
complaint the atoms are not in residue templates. And if I edit the
molecules, I only see boxes and it is without charges.
Creating new UNIT for residue: INT sequence: 117
Created a new atom named: C1 within residue: .R<INT 117>
Created a new atom named: H12 within residue: .R<INT 117>
Created a new atom named: H11 within residue: .R<INT 117>
Created a new atom named: C2 within residue: .R<INT 117>
Created a new atom named: H21 within residue: .R<INT 117>
Created a new atom named: H22 within residue: .R<INT 117>
Created a new atom named: C3 within residue: .R<INT 117>
Created a new atom named: H31 within residue: .R<INT 117>
Created a new atom named: H32 within residue: .R<INT 117>
Created a new atom named: C4 within residue: .R<INT 117>
Created a new atom named: H41 within residue: .R<INT 117>
Created a new atom named: H42 within residue: .R<INT 117>
Created a new atom named: C5 within residue: .R<INT 117>
Created a new atom named: H51 within residue: .R<INT 117>
Created a new atom named: H52 within residue: .R<INT 117>
Created a new atom named: C6 within residue: .R<INT 117>
Created a new atom named: H61 within residue: .R<INT 117>
Created a new atom named: H62 within residue: .R<INT 117>
total atoms in file: 2106
The file contained 2106 atoms not in residue templates

Any help is appreciated.

Andy

_________________________________________________________________
Find just what you are after with the more precise, more powerful new MSN
Search. http://search.msn.com.my/ Try it now.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu