problem in solvating the protein

From: sunita gupta (sunita.bio_at_gmail.com)
Date: Wed Dec 10 2008 - 06:14:50 CST

Hi all
I am simulating a big protein around 1050 residues. I got its proper pro.pdb
and pro.psf file with no error, but while i am solvating it using "package
require solvate" command with 5 A layer of water (total being 135222 atoms)
the TIP3 atoms after 99999 are not assigned and they are coming as***** in
waterbox.pdb file. Can anyone tell me that "Is 99999 is the maximum limit
after which no atomnumber can be assigned". In waterbox.psf all atom numbers
are fine.
The only problem os with the waterbox.pdb file....and part of it is shown
below

ATOM 99978 H2 TIP3 1081 88.622 43.066 126.344 1.00 0.00 WT6
H
ATOM 99979 OH2 TIP3 1082 100.257 31.925 136.245 1.00 0.00 WT6
O
ATOM 99980 H1 TIP3 1082 100.831 31.280 135.742 1.00 0.00 WT6
H
ATOM 99981 H2 TIP3 1082 100.956 32.318 136.787 1.00 0.00 WT6
H
ATOM 99982 OH2 TIP3 1085 88.413 35.969 138.488 1.00 0.00 WT6
O
ATOM 99983 H1 TIP3 1085 88.385 36.083 137.518 1.00 0.00 WT6
H
ATOM 99984 H2 TIP3 1085 87.777 36.684 138.783 1.00 0.00 WT6
H
ATOM 99985 OH2 TIP3 1090 93.163 32.602 138.990 1.00 0.00 WT6
O
ATOM 99986 H1 TIP3 1090 93.139 31.625 138.992 1.00 0.00 WT6
H
ATOM 99987 H2 TIP3 1090 94.098 32.752 139.335 1.00 0.00 WT6
H
ATOM 99988 OH2 TIP3 1096 100.265 37.855 103.878 1.00 0.00 WT6
O
ATOM 99989 H1 TIP3 1096 100.706 38.425 104.550 1.00 0.00 WT6
H
ATOM 99990 H2 TIP3 1096 99.799 37.246 104.406 1.00 0.00 WT6
H
ATOM 99991 OH2 TIP3 1097 90.168 40.896 132.714 1.00 0.00 WT6
O
ATOM 99992 H1 TIP3 1097 91.100 41.024 132.771 1.00 0.00 WT6
H
ATOM 99993 H2 TIP3 1097 89.913 40.357 133.531 1.00 0.00 WT6
H
ATOM 99994 OH2 TIP3 1098 83.692 37.818 108.835 1.00 0.00 WT6
O
ATOM 99995 H1 TIP3 1098 83.810 38.377 108.080 1.00 0.00 WT6
H
ATOM 99996 H2 TIP3 1098 82.931 37.287 108.501 1.00 0.00 WT6
H
ATOM 99997 OH2 TIP3 1099 93.282 43.438 125.010 1.00 0.00 WT6
O
ATOM 99998 H1 TIP3 1099 94.008 42.930 124.708 1.00 0.00 WT6
H
ATOM 99999 H2 TIP3 1099 92.676 42.771 125.361 1.00 0.00 WT6
H
ATOM ***** OH2 TIP3 1100 87.171 31.775 124.535 1.00 0.00 WT6
O
ATOM ***** H1 TIP3 1100 87.516 32.283 123.798 1.00 0.00 WT6
H
ATOM ***** H2 TIP3 1100 86.340 31.444 124.201 1.00 0.00 WT6
H
ATOM ***** OH2 TIP3 1101 92.262 45.661 119.667 1.00 0.00 WT6
O
ATOM ***** H1 TIP3 1101 91.630 45.692 120.432 1.00 0.00 WT6
H
ATOM ***** H2 TIP3 1101 92.047 46.462 119.197 1.00 0.00 WT6
H
ATOM ***** OH2 TIP3 1103 90.025 38.718 137.774 1.00 0.00 WT6
O
ATOM ***** H1 TIP3 1103 90.775 38.715 138.382 1.00 0.00 WT6
H
ATOM ***** H2 TIP3 1103 89.604 37.913 138.029 1.00 0.00 WT6
H
ATOM ***** OH2 TIP3 1104 81.811 39.781 129.484 1.00 0.00 WT6
O
ATOM ***** H1 TIP3 1104 82.583 40.235 129.911 1.00 0.00 WT6
H
ATOM ***** H2 TIP3 1104 81.490 39.124 130.132 1.00 0.00 WT6
H
ATOM ***** OH2 TIP3 1105 90.313 47.229 133.531 1.00 0.00 WT6
O
ATOM ***** H1 TIP3 1105 89.713 46.909 134.248 1.00 0.00 WT6
H
ATOM ***** H2 TIP3 1105 91.167 47.160 133.934 1.00 0.00 WT6
H

Any suggestion will be highly appretiated

Thanks and Regards

--
SUNITA GUPTA
Member Research Team
Lead Invent Technology
TBIU, IIT Delhi, India
Email- sunita_at_leadinvent.com
Ph- +9111 26581524 (Ex-6)

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