Re: Different resid in pdb fie but showing same molecule in VMD

From: Chitrak Gupta (
Date: Fri Jan 12 2018 - 19:00:01 CST

Hi Rabeta,

This looks like duplicate residue numbers. If you generated this structure
using psfgen and your molecule had > 9999 waters in the same segment,
psfgen ends up creating multiple waters with the same residue number.

The only way around that I know is manually re-segmenting the waters using
a tcl script. Basically, define waters 1 - 9999 as segment 1, waters 10000
- 19999 as segment 2 (renumber them from 1 to 9999) etc. That way psfgen
won't have to handle resid > 9999.

Hope this helps,

On Fri, Jan 12, 2018 at 6:42 PM, Rabeta Yeasmin <>

> Dear NAMD users,
> I am trying to visually track water molecules which pass through a channel
> formed a bilayer in VMD. I found that some water molecules with resid like
> 6b52, 6b7b, 6a22 are showed same water molecule in VMD although in pdb file
> they are shown as different resid and their coordinates are also different
> in pdb file. Water molecules with resid 314a, 314b, 314c also shows same
> molecule in vmd but have different resid in pdb file.
> I will be thankful if you anyone can explain this.
> Thanks very much.
> Rabeta Yeasmin

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