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

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Feb 02 2018 - 14:26:07 CST

Hi Chun,

I'm going to guess that you used CHARMM-GUI to setup your membrane. It has this nasty habit of putting more than 10000 residues in one segment, which overflows the 4 digits assigned to resid within a pdb. This causes a problem for psfgen, since it is looking for coordinates within the pdb that it will never find (ie the positions for the 10001st water residue). Instead, it will just overwrite coordinates it has already read in, leading to coordinates for your ghost residues placed at the origin. The easiest way to fix this is probably to use topotools (http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/, you'll want mergemols at the bottom) rather than psfgen to merge together the structure. If psfgen ever needs to touch the system (such as perhaps in an ionization step), you'll need to resegment your water with a script before you start:

set waterresidues [atomselect top "water"]
set newsegnames [list]
set postfix 0
for { set i 0 } { $i < [llength $waterresidues] } { incr i } {
    if { $i % 30000 == 0 } {
        incr postfix
    }
    lappend newsegnames W$postfix
}
$waterresidues set segname $newsegnames

-Josh

On 02/02/2018 09:23 AM, Chun Heung Wong wrote:
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 : Sun Sep 15 2019 - 23:19:24 CDT