VMD-L Mailing List

From: Salvatore Mario Cosseddu (S.M.Cosseddu_at_warwick.ac.uk)
Date: Thu Feb 14 2013 - 09:28:49 CST

Do you have a segment in the file i_s.psf that contains a water molecule
(TIP3) labeled in the resid field as 1000? Have a look if popc512.psf
contains a segment with the same name with a water labeled as 1000.

Regards
Salvatore

On 13/02/13 14:55, Mohammad Elgamacy wrote:
> Greetings,
>
> I have been trying to combine the PSF's of a small molecule and a large hydrated lipid patch (512 POPC and more than 17000 water molecules) but I keep getting a read error as I try to load the hydrated patch's PSF unto VMD, as follows:
>
>
>> Main< (cplx_setup) 9 % package require psfgen
>>
> 1.6
>
>> Main< (cplx_setup) 10 % readpsf i_s.psf
>>
> psfgen) reading structure from psf file i_s.psf
> psfgen) psf file does not contain cross-terms
>
>> Main< (cplx_setup) 11 % readpsf popc512.psf
>>
> psfgen) reading structure from psf file popc512.psf
> psfgen) Unable to add (duplicate?) residue TIP3:1000
>
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
>
> Do you have any idea why might this be happening and how can I get around it?
>
> Thanks in advance,
> Mohammad
>
> 

-- 
Salvatore Cosseddu
PhD student
Centre for Scientific Computing and School of Engineering
University of Warwick
Coventry CV4 7AL
United Kingdom
email: S.M.Cosseddu_at_warwick.ac.uk