VMD-L Mailing List

From: Pavan Ghatty (pavan.vmd_at_gmail.com)
Date: Sun Nov 27 2011 - 13:56:17 CST

Hello All,
I was recently trying to solvate a protein with the "solvate" package. It
did solvate the protein but the output pdb had the following lines. Towards
the end, the residue numbers of the water got weird. Is there a way to
ensure that the residue numbers are in increasing order?
I ended up cleaning the pdb file with a script and used it to add water in
Charmm but I was wondering if there was a more straightforward way.
Thanks,
PG

ATOM 85423 H1 TIP3W8800 82.710 20.118 -27.503 1.00 0.00 WT9
 H
ATOM 85424 H2 TIP3W8800 82.793 19.461 -28.846 1.00 0.00 WT9
 H
ATOM 85425 OH2 TIP3W9064 82.780 11.411 -8.145 1.00 0.00 WT9
 O
ATOM 85426 H1 TIP3W9064 82.608 12.274 -7.724 1.00 0.00 WT9
 H
ATOM 85427 H2 TIP3W9064 82.675 10.767 -7.455 1.00 0.00 WT9
 H
ATOM 85428 OH2 TIP3W 892 83.013 -33.351 45.007 1.00 0.00
 WT10 O
ATOM 85429 H1 TIP3W 892 83.018 -33.835 44.208 1.00 0.00
 WT10 H
ATOM 85430 H2 TIP3W 892 82.111 -32.989 45.013 1.00 0.00
 WT10 H
ATOM 85431 OH2 TIP3W6350 82.688 -7.297 33.259 1.00 0.00
 WT10 O
ATOM 85432 H1 TIP3W6350 82.688 -6.524 32.663 1.00 0.00
 WT10 H
ATOM 85433 H2 TIP3W6350 81.753 -7.458 33.368 1.00 0.00
 WT10 H
ATOM 85434 OH2 TIP3W8701 82.761 19.435 42.045 1.00 0.00
 WT10 O
ATOM 85435 H1 TIP3W8701 81.952 19.776 41.500 1.00 0.00
 WT10 H
ATOM 85436 H2 TIP3W8701 82.322 19.268 42.873 1.00 0.00
 WT10 H
ATOM 85437 OH2 TIP3W8800 82.796 19.251 37.538 1.00 0.00
 WT10 O
ATOM 85438 H1 TIP3W8800 82.710 20.118 37.917 1.00 0.00
 WT10 H
ATOM 85439 H2 TIP3W8800 82.793 19.461 36.574 1.00 0.00
 WT10 H
ATOM 85440 OH2 TIP3W 892 83.013 32.069 -20.412 1.00 0.00
 WT11 O
ATOM 85441 H1 TIP3W 892 83.018 31.584 -21.212 1.00 0.00
 WT11 H
ATOM 85442 H2 TIP3W 892 82.111 32.431 -20.407 1.00 0.00
 WT11 H
ATOM 85443 OH2 TIP3W 892 83.013 32.069 45.007 1.00 0.00
 WT12 O
ATOM 85444 H1 TIP3W 892 83.018 31.584 44.208 1.00 0.00
 WT12 H
ATOM 85445 H2 TIP3W 892 82.111 32.431 45.013 1.00 0.00
 WT12 H