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From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Jun 13 2012 - 05:41:27 CDT
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I just downloaded the CGenFF and browsed the file "top_all36_cgenff.rtf".
It seems that atom names *are *in fact always 4 characters our less. The
atom *types *designations are longer*. *So basically there is no problem. I
apologize for adding noise to the list.
On 13 June 2012 12:33, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com> wrote:
> Dear All,
>
> the CGenFF <http://mackerell.umaryland.edu/~kenno/cgenff/> is very useful
> for parametrizing small molecules. But since it contains so much data, the
> atom names are longer than four characters. This causes havoc with many
> programs that truncate atom names to 3 or 4 characters (Well actually the PDB
> standard <http://www.wwpdb.org/documentation/format32/sect9.html#ATOM>allows only four chars for the atom name). My question is:
>
> How can I prepare a PDB file with for use with psfgen? Will psfgen work
> with parameter sets, that contain atoms with long names?
>
> There was a related question<http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/0264.html>on the namd mailing list a while ago, but nobody answered, so I apologize,
> if I missed something obvious.
>
> Best Regards,
> Ajasja
>
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