From: Crowley, Michael (Michael.Crowley_at_nrel.gov)
Date: Wed Sep 16 2009 - 12:21:42 CDT

Dear vmd folks, this msg is for developers. The so-called amber7 prmtop format is designed for flexibility and allows for new data sections and different formats by specifying the field name and format for each field. It also allows the sections to be in any order. Will vmd be supporting this flexibility soon?

Our main concern is that we have added the ability to use current charmm ff to amber necessitating new ff sections and some different formats which all follow the prmtop standard. We are not able to read these prmtops into vmd. I do not know if it is just the title but that is where it fails now. Vmd appears to require the format to say 20a4 when we are using a80. Seems harmless from the amber stndpopint but breaks vmd.

If you can help at this time to get us going with the new prmtop, we can send an example prmtop/inpcrd. Thanks.
Best wishes, mike crowley


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________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu>
To: Luca Gelisio <luca.gelisio_at_gmail.com>; VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Sent: Wed Sep 16 07:01:57 2009
Subject: Re: vmd-l: segid WT100 is longer than 4 characters allowed by psf format

Hi Luca,

Surely. By changing from segid prefix from WT to W, you can increase the character space.
best,

Ramya


On Wed, Sep 16, 2009 at 3:34 AM, Luca Gelisio <luca.gelisio_at_gmail.com<mailto:luca.gelisio_at_gmail.com>> wrote:
Hi to all,

when generating a large solvation box (extension -> modeling -> add solvation box), keeping options "waterbox only" and "rotate to minimize volume", the error:
"segid WT100 is longer than 4 characters allowed by psf format"
appear on the terminal. I am running VMD on a i7 machine with a GTX285 plus a GTX295, 6 Gb RAM, on Linux Ubuntu (2.6.28-15).
The largest waterbox I have generated is 18x18x18 nm. Is it possible to generate a larger one?

Thanks,

luca