Dear Jason:
Here my late response to your email. I have installed ambertools 1.4
now. With tleap from this new installation, the same problem occur. The
ions are still outside the unit cell. The new sleap is now working with
my input after I applied all the bug fixes. I do not know what the plans
are for tleap in the future. But I would be grateful if this could be
fixed, especially since it worked in older versions.
Best regards.
Thomas
Jason Swails wrote:
> which leap are you using? sleap or tleap? I'm pretty sure that sleap
> required a bugfix, but that type of script worked just fine for me when I
> used sleap. It may also help if you can send some pictures showing us what
> you're talking about.
>
> Good luck!
> Jason
>
> On Fri, Jul 9, 2010 at 10:13 AM, Thomas Exner
> <thomas.exner.uni-konstanz.de>wrote:
>
>> Dear amber users,
>>
>> I am trying to simulate a protein-DNA complex. But I have some problems
>> to set up a water box with physiological salt concentration. Some of the
>> ions are placed outside of the box during the grid calculation. In a
>> periodic boundary simulation, these ions would lie in another box and
>> probably overlap there with some water molecules or even the solute of
>> this box. What is going wrong here and how can I fix this? The strange
>> thing is that the same input worked pretty fine with amber8. Here is the
>> input for leap:
>>
>> source leaprc.ff99bsc0
>> loadoff DCP_final.lib
>> loadoff MG.off
>> TAQ = loadpdb 3ktq.pdb
>> mods = loadAmberParams frcmod_phosphate
>> solvateoct TAQ TIP3PBOX 12
>> addions TAQ Na+ 66 Cl- 44
>> saveamberparm TAQ taq.top taq.xyz
>> quit
>>
>> Any help would be highly appreciated.
>>
>> Cheers,
>> Thomas
>>
>> --
>>
>> ________________________________________________________________________________
>>
>> Dr. Thomas E. Exner
>> Juniorprofessur "Theoretische Chemische Dynamik"
>> Fachbereich Chemie
>> Universität Konstanz
>> 78457 Konstanz
>>
>> Tel.: +49-(0)7531-882015
>> Fax: +49-(0)7531-883587
>> Email: thomas.exner.uni-konstanz.de
>>
>> ________________________________________________________________________________
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
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Received on Tue Aug 03 2010 - 04:30:04 PDT
