[gmx-users] top2psf with Amber99SB-ILDN

francesco oteri francesco.oteri at gmail.com
Thu Nov 22 18:26:42 CET 2012


yes,actually it works fine as long as you have one chain in you .top
file . if u have more subunits, u are supposed to merge the chains
using the appropriate value for -chainsep option in pdb2gmx

2012/11/22, Steven Neumann <s.neumann08 at gmail.com>:
> There was an error with index < 1 which this script assigned to bond
> part. The script provided here:
>
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/top2psf.pl
>
> works much better.
>
> Steven
>
> On Thu, Nov 22, 2012 at 12:50 PM, francesco oteri
> <francesco.oteri at gmail.com> wrote:
>> hi,it would be nice knowing the errors.
>>
>> Francesco
>>
>>
>> 2012/11/22, Steven Neumann <s.neumann08 at gmail.com>:
>>> Dear Gmx Users,
>>>
>>> Is it possible to convert topology produced by Gmx and convert it ont
>>> the psf file? I used Justin script but when I load pdb and psf in VMD
>>> then there are some errors.
>>> Would you help?
>>>
>>> Steven
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>>
>>
>> --
>> Cordiali saluti, Dr.Oteri Francesco
>> --
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-- 
Cordiali saluti, Dr.Oteri Francesco



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