Hi Ross and Raja
I followed Ross instructions and reinstalled Amber 9 (fortunately we
also had this version) from scratch using intel compiler. The solvation
box looks OK now.
thanks for your help
Eric
Ross Walker a écrit :
> Hi Eric,
>
> This is a known problem with earlier versions of AMBER and specific
> compilers. E.g.
>
> http://archive.ambermd.org/200406/0165.html
>
> I suspect you are hitting the same compiler bug. The quickest solution would
> probably be to download the latest copy of AMBERTools from the AMBER Website
> and compile xleap in there using gnu or Intel compilers. The problem will
> then likely go away.
>
> Alternatively I would try recompiling AMBER 8 with a different set of
> compilers.
>
> All the best
> Ross
>
>
>> -----Original Message-----
>> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
>> Behalf Of pellegrini
>> Sent: Tuesday, March 23, 2010 6:11 AM
>> To: amber.ambermd.org
>> Subject: [AMBER] Problem with solvationbox command
>>
>> Hello evrybody,
>>
>> I justed posted a few hours ago about a problem encountered when
>> solvating a protein with a
>> sugar-ligand. Sorry, but in my previous post, I was perhaps too fuzzy.
>>
>> Using the following commands on the first attached PDB file (ADA.pdb):
>>
>> source leaprc.ff99
>> source leaprc.Glycam_06
>> x = loadPDB ADA.pdb
>> solvateBox x TIP3PBOX 10.0
>> addions x Na+ 0
>> saveAmberParm x ADA_Solvated.top ADA_Solvated.crd
>> savePDB x ADA_Solvated.pdb
>>
>> creates a weird solvation box that does not surround the solute at all
>> as you can see when looking at the second attached file
>> (ADA_Solvated.pdb). Would you have any clue of what is (or I did) wrong
>> with my setup ?
>>
>> thank you very much
>>
>> Eric
>>
>
>
>
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Received on Wed Mar 24 2010 - 03:30:03 PDT
