RE: problem in solvating the protein

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Dec 10 2008 - 08:13:06 CST

The problem is the fixed width format for pdbs. Since a pdb can only have
five columns for index, no number after 99,999 can be written properly. A
psf file does not have these restrictions. However, it’s nothing to worry
about; both VMD and NAMD ignore the indices in the file and set their own
anyway.

From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of sunita gupta
Sent: Wednesday, December 10, 2008 6:15 AM
To: namd-l_at_ks.uiuc.edu; vmd_at_ks.uiuc.edu
Subject: namd-l: problem in solvating the protein

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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