RE: Autopsf error with a modified top file

From: CHINDEA Vlad (vchindea_at_hotmail.com)
Date: Sat Feb 21 2009 - 06:04:19 CST

Hi Peter

 

It worked ! When using a pgn script in TkCon, as I did finally, it seems that also residue ID is a must not only the residue name !

 

I must say that Autopsf Tk error messages are a bit strange and not very helpful (at least for me). I could not have done it without your interpretation of the VMD error messages.

 

Many thanks and all the best

 

Vlad

 

> Date: Fri, 20 Feb 2009 23:19:22 -0600
> From: petefred_at_ks.uiuc.edu
> To: vchindea_at_hotmail.com
> CC: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: Autopsf error with a modified top file
>
> Hi Vlad,
> psfgen must have residue names in order to build a psf; otherwise, how
> is it supposed to know what residue a given collection of atoms is
> supposed to be? You should be ok without the other fields, so long as
> autopsf split the chains properly. You will need to be exceedingly
> careful to keep your columns aligned properly as you add in the residue
> name; please be sure to consult the pdb file format reference available
> from rcsb.org.
>
> Best,
> Peter
>
>

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