Tutorial-l Mailing List

From: Timothy Isgro (timisgro_at_ks.uiuc.edu)
Date: Tue Nov 07 2006 - 16:53:16 CST

Hi Won-Young,
I don't think that spacing should be an issue. That is, I would not
expect a program like psfgen to produce an error when two spaces are
placed between subsequent atoms instead of one space. For
simplicity, however, try recreating your bond entries with single
spaces between atom names. Psfgen knows that each pair of atoms
after the BOND command is to be bonded. You need not separate one
bonded pair from another with two spaces or a tab, for instance.
(Make sure you have the proper atom names listed, an even amount of
atoms per BOND entry, etc.). For the information of everyone, the
format should be as follows. Your formatting appears fine to me, but
try generating it from scratch with single spaces.

 From the topology file tutorial:
http://www.ks.uiuc.edu/Training/Tutorials/

"BOND CB CA N HN N CA
indicates sets of 2 atoms which are connected by a single bond. The
bonds are created between consecutive atoms. Thus, one bond is placed
between atoms CB and CA, one is placed between N and HN, and one
between N and CA. The BOND entries on the next line are read exactly
the same way, and are put on a new line simply for readability."

-Tim

On Nov 7, 2006, at 2:20 PM, Won-Young Ahn wrote:

> Dear NAMD users,
>
>
>
> While I was creating a topology for a new residue, I met a problem
> of arranging spaces between atoms.
>
> Could someone inform me how many spaces I should put between atoms?
>
>
>
> An example of BOND table lines were attached below.
>
>
>
> BOND C1 C2 C1 C20 C1 O2 C1 H17 C2 C3
>
> BOND C2 C14 C2 H18 C3 C21 C3 C22 C3 H19
>
>
>
> Thanks,
>
>
>
> Won-Young
>
>

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