Double-defined segid, resid for more than 9999 id's

From: Chun Heung Wong (w.chunheung_at_gmail.com)
Date: Fri Feb 02 2018 - 10:17:30 CST

Dear users,

I am getting problems whilst adapting the KCSA membrane tutorial to my own
setup:

mol delete all
package require psfgen
resetpsf
topology ../c32b1/toppar/top_all27_prot_lipid.rtf
readpsf membrane.psf
coordpdb membrane.pdb

readpsf protein.psf
coordpdb protein.pdb

writepdb ./output/newprotein.pdb
writepsf ./output/newprotein.psf

In this code, I attempt to load in two different sets of pdb/psf files and
merge them using psfgen. However, upon inspecting the resulting
newprotein.pdb file I have noticed that the resid's go up to 9999 and
reset back to 1, resulting in particles with the same resid, and segid

ATOM 68801 H1 TIP3 9998 -42.735 29.263 -29.720 1.00 0.00
TIP3
ATOM 68802 H2 TIP3 9998 -44.123 28.703 -29.491 1.00 0.00
TIP3
ATOM 68803 OH2 TIP3 9999 -41.689 34.251 -28.829 1.00 0.00
TIP3
ATOM 68804 H1 TIP3 9999 -40.939 34.095 -29.402 1.00 0.00
TIP3
ATOM 68805 H2 TIP3 9999 -42.028 35.103 -29.104 1.00 0.00
TIP3
ATOM 68806 OH2 TIP3 0 -37.273 32.066 -23.800 1.00 0.00
TIP3
ATOM 68807 H1 TIP3 0 -37.081 31.135 -23.912 1.00 0.00
TIP3
ATOM 68808 H2 TIP3 0 -36.416 32.491 -23.811 1.00 0.00
TIP3
ATOM 68809 OH2 TIP3 1 -35.957 34.855 -25.723 1.00 0.00
TIP3
ATOM 68810 H1 TIP3 1 -36.238 35.564 -26.300 1.00 0.00
TIP3
ATOM 68811 H2 TIP3 1 -35.014 34.782 -25.874 1.00 0.00
TIP3
ATOM 68812 OH2 TIP3 2 -45.205 31.640 -24.649 1.00 0.00
TIP3
ATOM 68813 H1 TIP3 2 -45.972 31.108 -24.860 1.00 0.00
TIP3
ATOM 68814 H2 TIP3 2 -44.526 31.330 -25.249 1.00 0.00
TIP3

In the subsequent step of removing overlapping/unwanted atoms, this gives
some problems. Why does this happen and how can I fix this?

Yours sincerely,

Chun Heung Wong

This archive was generated by hypermail 2.1.6 : Thu Sep 19 2019 - 23:19:24 CDT