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

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Mon Jan 15 2018 - 01:57:54 CST

Dear Gupta,

Thank you very much for your information. Actually, I have created the psf
and pdb file from CHARMM-GUI website.

Rabeta Yeasmin

On Fri, Jan 12, 2018 at 7:00 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:

> 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,
> Chitrak.
>
> On Fri, Jan 12, 2018 at 6:42 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
> wrote:
>
>> 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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