Dear AMBERs,
the protein looks like this:
ATOM first
ATOM ...
ATOM last
TER
ION1
TER
ION2
TER
etc.
TER
WATER1 = ATOM 1 O WAT 312
ATOM 2 H1 WAT 312
ATOM 3 H2 WAT 312
WATER2
etc. (no TER between waters)
----------------------------------
a Leap session looks like this:
xxx = loadpdb protein_wat.pdb
solvatebox xxx WATBOX216 10
saveamberparm xxx xxx.top xxx.crd
But the crystal waters are in the xxx.top file stored as IP3 waters
(rezidue name changed from WAT --> IP3) and the other box waters are
stored as WAT (I think that both are TIP3 waters). Is it correct? But I
prefer the same names for crystal and box waters. Must I create new
rezidue named WAT as described in manual? Or does exist another way?
Thank you very much in advance,
Michal Otyepka
*---------------------------------------------[*]-*
| Department of Inorganic and Physical Chemistry |
| Palacky University |
| tr. Svobody 26, 771 46 Olomouc, Czech Republic |
| |
|ph. +420 68 5222451 (+396) fax +420 68 522 5737|
| fax +420 68 563 4420|
|
http://aix.upol.cz/~otyepka |
|
http://www.upol.cz/kafch |
*-------------------------------------------------*
Received on Mon Feb 26 2001 - 23:35:42 PST
