AMBER Archive (2008)

Subject: AMBER: solvateOct produces strange residues compared to solvateCap

From: Markus Kaukonen (mka_at_fyslab.hut.fi)
Date: Fri Apr 04 2008 - 03:08:53 CDT

Dear All,

I generated old style prep and parm files for a
H5O2 complex (a proton shared by 2 waters).
(as a lazy man still waiting for the TUTORIAL A1: Non-standard Residues
(Includes charge fitting)[Coming soon.] )

When solvating this molecule using tleap and solvateCap (AMBER9)
everything is fine but when using instead
solvateOct or sovateBox or solvateDontClip the first (H5O2) residue is
split into pieces.

My initial pdb file:
ATOM 1 O1 2WH 1 0.000 -0.019 1.209
ATOM 2 H11 2WH 1 0.809 0.145 1.736
ATOM 3 H12 2WH 1 -0.809 0.145 1.735
ATOM 4 H+ 2WH 1 0.000 0.020 0.000
ATOM 5 O2 2WH 1 0.000 -0.019 -1.209
ATOM 6 H21 2WH 1 0.809 0.145 -1.735
ATOM 7 H22 2WH 1 -0.809 0.145 -1.736
END

'Good' result (with solvateCap), beginning of the solvated pdb file:
REMARK
ATOM 1 O1 2WH 1 0.000 -0.019 1.209 -0.8167 1.500
ATOM 2 1H1 2WH 1 0.809 0.145 1.736 0.5108 1.200
ATOM 3 2H1 2WH 1 -0.809 0.145 1.735 0.5107 1.200
ATOM 4 H+ 2WH 1 0.000 0.020 0.000 0.5904 1.200
ATOM 5 O2 2WH 1 0.000 -0.019 -1.209 -0.8167 1.500
ATOM 6 1H2 2WH 1 0.809 0.145 -1.735 0.5107 1.200
ATOM 7 2H2 2WH 1 -0.809 0.145 -1.736 0.5108 1.200
TER
ATOM 8 O WAT 2 2.674 5.639 4.323 -0.8340 1.500
ATOM 9 H1 WAT 2 1.785 5.981 4.221 0.4170 1.200
ATOM 10 H2 WAT 2 2.958 5.439 3.431 0.4170 1.200
TER
--------CLIP---------

'Bad' result (with solvateOct), beginning of the solvated pdb file:
REMARK
ATOM 1 O1 2WH 1 9.871 9.149 10.727 -0.8167 1.500
ATOM 2 1H1 2WH 1 9.939 8.456 11.415 0.5108 1.200
ATOM 3 2H1 2WH 1 9.005 9.117 10.271 0.5107 1.200
TER
ATOM 4 H+ 2WH 1 10.546 10.152 10.755 0.5904 1.200
ATOM 5 O2 2WH 1 11.267 11.123 10.727 -0.8167 1.500
ATOM 6 1H2 2WH 1 11.943 11.289 11.415 0.5107 1.200
TER
ATOM 7 2H2 2WH 1 11.009 11.951 10.271 0.5108 1.200
ATOM 8 O WAT 2 6.360 7.817 16.605 -0.8340 1.500
ATOM 9 H1 WAT 2 5.709 8.403 16.219 0.4170 1.200
TER
ATOM 10 H2 WAT 2 7.155 8.348 16.665 0.4170 1.200
ATOM 11 O WAT 3 7.838 5.506 17.142 -0.8340 1.500
ATOM 12 H1 WAT 3 7.203 5.580 17.854 0.4170 1.200
--------CLIP---------

My new residue is now mysteriously cut into 3 pieces and all the waters
are messed up!

What is going on? Any help appreciated!

Terveisin Markus

My prep file

    0 0 2
2wh.dat
2H2O and H+ b3lyp vac ri def2-sv(p)
2wh.dat
  2WH INT 1
 CHANGE OMIT DU BEG
   0.00000
   1 DUMM DU M 0.0000 0.0000 .0000 .0000
   2 DUMM DU M 0.0000 1.0000 .0000 .0000
   3 DUMM DU M 1.0000 1.0000 .0000 .0000
   4 O1 o1 B 0.0000 -0.0189 1.2089 -0.816705
   5 H11 h1 E 0.8089 0.1453 1.7356 0.510764
   6 H12 h1 E -0.8090 0.1453 1.7354 0.510738
   7 H+ h2 E 0.0000 0.0204 0.0000 0.590404
   8 O2 o1 B 0.0000 -0.0189 -1.2089 -0.816702
   9 H21 h1 E 0.8090 0.1453 -1.7354 0.510736
  10 H22 h1 E -0.8088 0.1453 -1.7356 0.510764

DONE
STOP

My Params file

2H2O and H+ in the middle

MASS
o1 15.999
h1 1.008
h2 1.008

BOND
o1-h1 507.707 0.97911
o1-h2 74.327 1.20952

ANGLE
h1-o1-h1 54.538 111.417
h1-o1-h2 51.595 122.148
o1-h2-o1 16.672 176.270

DIHEDRAL
h1-o1-h2-o1 1 0.094 0.000 2. ! 0.38 2 1

NONB
o1 1.6612 0.2100 ! parm99: O (OPLS)
h1 0.6000 0.0157 ! parm99: H (Veenstra)
h2 0.6000 0.0157 ! parm99: H (Veenstra)

tleap commands for 'ok' structure

logfile logfil
source leaprc.ff03
addPath /home/mka/Data/Amber
loadAmberPrep 2wh.in
loadAmberParams 2wh.dat
x=loadpdb init.pdb
solvateCap x TIP3PBOX {0 0 0} 12.0 2.0
check x
saveamberparm x prmtop prmcrd
quit

tleap commands for the 'bad' structure, the only difference is the
solvate... line

logfile logfil
source leaprc.ff03
addPath /home/mka/Data/Amber
loadAmberPrep 2wh.in
loadAmberParams 2wh.dat
x=loadpdb init.pdb
solvateOct x TIP3PBOX 7
check x
saveamberparm x prmtop prmcrd
quit 

-- 
-----------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   \____+358-(0)45-1242068/mob
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