Hi rmv,

i have gone through your script could not understand below part
read univ
* modified pdb
*
pdb
segid 22 1
ires 23 4
w 61 6
end

Also i am having problem with my water box which i created using charmm-GUI. dims 30*30*30.

The problem is i am getting two segid in the box and am not able to create psf for the pdb.

this is the small part of my water box

Code:
ATOM   1591  OH2 TIP3  541       6.691   5.318   1.346  1.00  0.00      WZ1
ATOM   1592  H1  TIP3  541       6.325   4.552   1.788  1.00  0.00      WZ1
ATOM   1593  H2  TIP3  541       7.604   5.347   1.632  1.00  0.00      WZ1
ATOM   1594  OH2 TIP3  542       8.664   4.668   2.881  1.00  0.00      WZ1
ATOM   1595  H1  TIP3  542       9.563   4.394   2.697  1.00  0.00      WZ1
ATOM   1596  H2  TIP3  542       8.277   3.926   3.346  1.00  0.00      WZ1
ATOM   1597  OH2 TIP3    1      -3.044  -4.896  10.643  1.00  0.00      WZ2
ATOM   1598  H1  TIP3    1      -2.955  -3.952  10.510  1.00  0.00      WZ2
ATOM   1599  H2  TIP3    1      -3.683  -5.171   9.985  1.00  0.00      WZ2
ATOM   1600  OH2 TIP3    2      -4.111  -5.641  14.062  1.00  0.00      WZ2
ATOM   1601  H1  TIP3    2      -4.150  -6.287  14.767  1.00  0.00      WZ2
ATOM   1602  H2  TIP3    2      -4.434  -6.107  13.290  1.00  0.00      WZ2
ATOM   1603  OH2 TIP3    4      -0.405  -2.702  12.363  1.00  0.00      WZ2
ATOM   1604  H1  TIP3    4      -0.846  -3.422  12.814  1.00  0.00      WZ2
ATOM   1605  H2  TIP3    4      -0.418  -1.981  12.993  1.00  0.00      WZ2



i would like to have only 1 segid in my pdb as well as psf.

! Read sequence from pdb file, generate segment, and read coordinates.
open read card name "waterbox.pdb" unit 12
read segid WZ1 PDB unit 12

but it reads all 855 residues instead of only reading segment WZ1 which has 542 water molecules.

How can i create pdb as well as psf from above pdb in charmm to get single segid for whole water box.

Thank-you,
Regards,
Rohit


Edited by Rohit (11/23/17 12:57 AM)