From: Yi Wang, PhD (dexterwy_at_gmail.com)
Date: Mon Mar 04 2013 - 22:10:47 CST
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I'm not quite familiar with this. But I vaguely recall the PDB format leaves four digits for residue number. For adding more than 9999 waters, different chain name is created. Could this be the cause, that the plugin is trying to add more than 9999 residues to the same chain?
___________________________
Yi (Yves) Wang, PhD
On 2013-3-5, at 上午11:37, Sridhar Kumar Kannam wrote:
> Hi Fellow researchers,
>
> I have created a graphene layer using VMD nanotube builder I am getting a strange problem when I am trying to solvate it.
>
> My very simple script is below ...
>
>
> graphene -lx 20 -ly 20 -type zigzag -nlayers 1 -b 1 -a 0 -d 0 # creates a graphene layer
> set all [atomselect top all]
> $all set segname X
> $all writepsf graphene.psf
> $all writepdb graphene.pdb
> solvate graphene.psf graphene.pdb -z 5 +z 5 -o solvate
>
>
> The above script is working fine when my graphene dimentions are below 15 and 15 which will have less than 10000 carbon atoms.
> for example with this line the script is working fine - graphene -lx 15 -ly 15 -type zigzag -nlayers 1 -b 1 -a 0 -d 0
>
> So I thought the problem could be due to more than 10000 residues (nanotube builder is giving a new residue id to each carbon atoms)
> I set all the carbon atoms residues to "1" by using the command - $all set resid 1 - before writing the above psf and pdb files...
> But it did not help ...
>
> Can anyone please give me a clue ....
>
>
>
> --
> Cheers !!!
> Sridhar Kumar Kannam :)
>
>
>
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