AMBER Archive (2006)

Subject: AMBER: ptraj dumpq feature/bug

From: Markus Kaukonen (markus.kaukonen_at_teokem.lu.se)
Date: Thu Aug 24 2006 - 03:31:51 CDT

Dear All,

I convert from mdrest format to pdb format with
'ambpdb -pqr -p hboth.prmtop < mdrest7 > mdrest7.pdb'
in the output pdb file 'mdrest7.pdb' one has:
/....
ATOM 15277 O WAT 1006 16.453 -9.102 8.566 -0.8196 1.500
ATOM 15278 H1 WAT 1006 17.625 -10.256 8.202 0.4564 1.200
ATOM 15279 H2 WAT 1006 16.849 -8.812 9.406 0.3781 1.200
...
ATOM 15826 O WAT 1189 8.566 16.453 -9.102 -0.8196 1.500
ATOM 15827 H1 WAT 1189 8.202 17.625 -10.256 0.4564 1.200
ATOM 15828 H2 WAT 1189 9.406 16.849 -8.812 0.3781 1.200
...
ATOM 16375 O WAT 1372 -9.102 8.566 16.453 -0.8196 1.500
ATOM 16376 H1 WAT 1372 -10.256 8.202 17.625 0.4564 1.200
ATOM 16377 H2 WAT 1372 -8.812 9.406 16.849 0.3781 1.200
...../

That is, some waters with special charges. This is ok.
Now I try to strip all other waters except the ones listed above by:
'ptraj hboth.prmtop ptraj_mdrest_pdb_noH2O.in'
file ptraj_mdrest_pdb_noH2O.in contains/:
trajin mdrest7
trajout mdrest7_noH2O.pdb pdb dumpq
strip :1373-99999
strip :1190-1371
strip :1007-1188
go/

Now (in the file 'mdrest7_noH2O.pdb.1' the three waters
listed above are there with the correct xyz positions,
BUT WITH THE WRONG CHARGES for the last 2 waters:
ATOM 15277 O WAT 1006 16.453 -9.102 8.566 -0.8196 1.6612
ATOM 15278 H1 WAT 1006 17.625 -10.256 8.202 0.4564 0.6000
ATOM 15279 H2 WAT 1006 16.849 -8.812 9.406 0.3781 0.6000
ATOM 15280 O WAT 1007 8.566 16.453 -9.102 -0.8340 1.6612
ATOM 15281 H1 WAT 1007 8.202 17.625 -10.256 0.4170 0.6000
ATOM 15282 H2 WAT 1007 9.406 16.849 -8.812 0.4170 0.6000
ATOM 15283 O WAT 1008 -9.102 8.566 16.453 -0.8340 1.6612
ATOM 15284 H1 WAT 1008 -10.256 8.202 17.625 0.4170 0.6000
ATOM 15285 H2 WAT 1008 -8.812 9.406 16.849 0.4170 0.6000/

What did I do wrong or is this a feature/bug?

Terveisin, Markus 

-- 
-----------www= http://www.iki.fi/markus.kaukonen---------------
Markus.Kaukonen_at_teokem.lu.se  \ HOME->   Viinirinne 3 F 12
Dep. of Theoretical Chemistry  \_______  02630 Espoo, Finland
Lund University                 \ tel:+358-(0)9-5127122/h
Chemical Centre, P. O. Box 124   \____
S-221 00, Lund, Sweden             \______ H+ ______
--- Rikos ei kannata, eika maatalous Suomessa. (Paimio 1998) ---

-- 
-----------www= http://www.iki.fi/markus.kaukonen---------------
Markus.Kaukonen_at_teokem.lu.se  \ HOME->   Viinirinne 3 F 12
Dep. of Theoretical Chemistry  \_______  02630 Espoo, Finland
Lund University                 \ tel:+358-(0)9-5127122/h
Chemical Centre, P. O. Box 124   \____
S-221 00, Lund, Sweden             \______ H+ ______
--- Rikos ei kannata, eika maatalous Suomessa. (Paimio 1998) ---

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