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

From: Chun Heung Wong (w.chunheung_at_gmail.com)
Date: Wed Feb 07 2018 - 10:59:28 CST

Problem resolved by splitting the large .pdb file in seperate, smaller .pdb
files with indexes lower than 9999 e.g. per segment. These then need to be
iteratively loaded into psfgen. Aparently psfgen doesn't handle indexes
above 9999 very well for identical segment names.

Yours sincerely,

Chun Heung Wong

On 2 February 2018 at 17:17, Chun Heung Wong <w.chunheung_at_gmail.com> 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
>

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