VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Nov 27 2011 - 15:00:26 CST

On Sun, Nov 27, 2011 at 2:56 PM, Pavan Ghatty <pavan.vmd_at_gmail.com> wrote:
> 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

the are not weird. it only so happens that the solvent section is
generated by periodically replicating the reference solvent block
(each block as a separate segment) and then cutting away the
parts that overlap or are outside the desired volume.

> ensure that the residue numbers are in increasing order?

why would that be needed? NAMD doesn't care.
each residue is still uniquely identified by segment id
and residue number. what else do you want?

axel.

> 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 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.