VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Nov 24 2014 - 16:47:27 CST

Hi Mihaela,
Use the development versions of VMD (1.9.2b1 or later). 1.9.1 did not
handle long atomtypes very well at all, and would truncate atomtypes at
4 characters when writing out psf files. This has been fixed in 1.9.2.
-Josh Vermaas

On 11/23/14, 5:06 PM, Mihaela Drenscko wrote:
> Hello,
>
> I am using topotools to merge two parts, one PS and one solvent. This
> is how the psf of PS looks like before merge:
> 1 PS 1 PSH CG CG2R61 0.000000 12.0110 0
> 2 PS 1 PSH CD1 CG2R61 -0.115000 12.0110 0
> 3 PS 1 PSH HD1 HGR61 0.115000 1.0080 0
> 4 PS 1 PSH CD2 CG2R61 -0.115000 12.0110 0
> 5 PS 1 PSH HD2 HGR61 0.115000 1.0080 0
> 6 PS 1 PSH CE1 CG2R61 -0.115000 12.0110 0
>
> After merge, atom types are truncated, thus:
>
> 1 PS 1 PSH CG CG2R 1.000000 12.0107 0
> 2 PS 1 PSH CD1 CG2R 1.000000 12.0107 0
> 3 PS 1 PSH HD1 HGR6 0.115000 1.0079 0
> 4 PS 1 PSH CD2 CG2R 1.000000 12.0107 0
> 5 PS 1 PSH HD2 HGR6 0.115000 1.0079 0
> 6 PS 1 PSH CE1 CG2R 1.000000 12.0107 0
>
> What can I do to keep the atom types the same as before merging?
>
> Thank you,
> Mihaela
>