Just a note about this... whether sleap considers the ions as part of the solute or solvent depends on the order in which you add ions and solvate.
If you addIons then solvateBox, sleap considers the ions to be solute.
But if you solvateBox then addIons, sleap considers the ions to be solvent.
(This was the case in the leap input files provided here as a test case for the sleap/iwrap issue)
tleap considers the ions to be solute regardless of the order you add ions/solvate.
As the test case displays this behavior with Na=solute, and Na=solvent, this doesn't appear to be the cause of the sleap/iwrap issue.
Jodi
On Apr 8, 2011, at 2:30 PM, B. Lachele Foley wrote:
> One difference: tleap considers the two Na+ ions to be part of the solute. Sleap puts them in the solvent.
>
> I can see arguments both ways... but, that might be part of the issue.
>
> :-) 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 2:17 PM
> To: AMBER Developers Mailing List
> Subject: Re: [AMBER-Developers] Problems with sleap and iwrap
>
> Hi Ross,
>
> 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?
>
> and I agree with Jason and Lachele that the problem seems to be with the section "SOLVENTS_POINTER"
>
> Sincerely,
>
> Wei
>
> On Apr 8, 2011, at 11:58 AM, Ross Walker wrote:
>
>> Hi All,
>>
>> Has anybody experienced problems with sleap and iwrap? (Is anybody using
>> sleap routinely?).
>>
>> Attached is a pdb file and two scripts that 'should' do the same thing in
>> sleap and tleap. If you then run MD with the two resulting prmtop and inpcrd
>> files things appear to be fine without iwrap=0 but if you set iwrap=1 the
>> sleap generated prmtop run behaves VERY strangely.
>>
>> You get the protein jumping out of the water box in a strange way. For this
>> case with just one molecule things appear to be ok, as in just a strange
>> imaging issue. However, if you set a system up with glycans attached then in
>> the sleap run only half the molecule gets imaged and then it crashes with
>> vlimit errors (due to bonds being massively stretched) as soon as you turn
>> on iwrap.
>>
>> Hence it seems like there is something very wrong with the prmtop generated
>> by sleap. This is BAD since sleap is the only way to generate prmtops with
>> mixed 1-4 scaling parameters in right now.
>>
>> Has anybody else seen such issues / has an idea of what might be wrong with
>> the sleap prmtop?
>>
>> 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 |
>> ---------------------------------------------------------
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>> be read every day, and should not be used for urgent or sensitive issues.
>>
>>
>> <originalt.pdb><leaprc_pdb_tleap.txt><leaprc_pdb_sleap.txt><run_EQMD.sh>_______________________________________________
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Received on Fri Apr 08 2011 - 16:30:04 PDT
