> as for the ATOMS_PER_MOLECULE section, sleap and tleap are identical.
Identical, and correct. I just ran a check. Other than the thing I mentioned before about the sodiums, that's the diff I see WRT solvent pointers.
The BOX_DIMENSIONS are slightly smaller in sleap, but that's probably not the cause of the trouble.
Ross, could you send us the GP one -- that's the sort of thing I recall us seeing before. But, I think that might be a different issue from this.
Does it happen with sander? I often find that trying something using both programs will result in a more useful set of errors...
:-) Lachele
Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
lfoley.uga.edu
http://glycam.ccrc.uga.edu
________________________________________
From: Wei Zhang [zgjzweig.gmail.com]
Sent: Friday, April 08, 2011 3:04 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] Problems with sleap and iwrap
as for the ATOMS_PER_MOLECULE section, sleap and tleap are identical.
On Apr 8, 2011, at 1:52 PM, Ross Walker wrote:
> Hi Wei,
>
>> I was trying to run the script run_MDEQ.sh, but it is missing a
>> file "fixedgroups".
>> Can you send the other file so I can reproduce the error?
>
> The person I was working with who saw this problem and provided me with the
> scripts did not include this. However, it is not needed to see the issue.
> Just remove it from the script and set ntr=0.
>
>> and I agree with Jason and Lachele that the problem seems to be with
>> the section "SOLVENTS_POINTER"
>
> I agree, I think the two most likely culprits are the solvent pointers and
> the section that defines the atoms per molecule. The real problem occurs
> when one has glycans bound to the protein. Then both sander and pmemd image
> the glycan without imaging the rest of the molecule and things blow up
> because you end up with hugely stretched bonds. This to me looks like the
> glycans are not placed in the same molecule as the protein but I haven't had
> time to sit and properly look at it.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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Received on Fri Apr 08 2011 - 12:30:10 PDT
