[gmx-users] make_ndx and residue name length

[Alan Dodd]

Thanks... I think I'll just get the CVS make_ndx and integrate that into my current CVS copy, rather than try to hunt the different locations down!

----- Original Message ----
From: Berk Hess <gmx3 at hotmail.com>
To: gmx-users at gromacs.org
Sent: Wednesday, September 5, 2007 11:22:15 AM
Subject: RE: [gmx-users] make_ndx and residue name length




>From: Alan Dodd <anoddlad at yahoo.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] make_ndx and residue name length
>Date: Tue, 4 Sep 2007 10:55:07 -0700 (PDT)
>
>The maximum permissible residue name length is at least 5 characters long 
>for a tpr or gro, but the length of residue name permitted by make_ndx is 
>only 4 characters.  And of course, pdb should have only 3 characters.  
>While I can change the names in a gro or a pdb quite quickly and easily, is 
>there a way to change this in a tpr?  I'm currently getting around the 
>problem by converting tprs to pdbs for use by make_ndx, but it's messy...  
>Alternatively, is there any fundamental reason why the string in make_ndx 
>inputs is less than that for files, or can I safely bump up the relevant 
>digit in the code and recompile?

I did not know about this check, but now that I have looked at the code it 
seems I have
programmed it myself a decade ago.
The only reason for a limit was/is programming convenience.
You can change it and recompile, but be careful that the number 5 occurs at 
multiple places
in make_ndx.c

I was too lazy to remove the limit, so I have set it to 30 now in the CVS 
(and also put defined
this number in one place only).

Berk.

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