Hi,
Since you're having issues with tleap, you may want to try the
carbohydrate builder from
http://glycam.org/
-Dan
On Tue, Jan 5, 2016 at 11:11 AM, Levan Tsereteli
<Levan.Tsereteli.mpikg.mpg.de> wrote:
> Thanks Jason
>
> To build system by adding chunks its working however tail and head dont find each other properly. And I don't really know how to make tleap recognize proper positions. The error when building longer systems is very strange. I will write it here more specifically may be somebody has encountered it already. So when I want to build up 122 monomers its failing with "sequence: Improper number of arguments!" comment:
>
> sequence: Improper number of arguments!
> usage: sequence <LIST>
> impose: Argument #1 is type String must be of type: [unit]
> usage: impose <unit> <residueseqlist> <internalslistlist>
> impose: Argument #1 is type String must be of type: [unit]
> usage: impose <unit> <residueseqlist> <internalslistlist>
> impose: Argument #1 is type String must be of type: [unit]
> usage: impose <unit> <residueseqlist> <internalslistlist>
> sugar: expected 'default'
> usage: set <container> <parameter> <object>
> or: set default <parameter> <value>
> saveAmberParm: Argument #1 is type String must be of type: [unit]
> usage: saveAmberParm <unit> <topologyfile> <coordfile>
> saveMol2: Argument #1 is type String must be of type: [unit]
> usage: saveMol2 <object> <filename> <option>
> <option> = 0 for Default atom types
> <option> = 1 for AMBER atom types
> Quit
>
>
> And when units are more then 122 even for 123, its failing with:
>
> Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
> ERROR: syntax error
>
> ERROR: syntax error
>
> ERROR: syntax error
>
> ERROR: syntax error
>
>
>
> For the less then 122 units its all ok.
>
> May be somebody had the similar problem ?
>
>
> Thanks a lot
>
> levan
>
>
>
> ________________________________________
> From: Jason Swails [jason.swails.gmail.com]
> Sent: 05 January 2016 17:57
> To: AMBER Mailing List
> Cc: david.case.rutgers.edu
> Subject: Re: [AMBER] Problems with tleap when generating gib structures
>
> On Tue, Jan 5, 2016 at 11:51 AM, Levan Tsereteli <
> Levan.Tsereteli.mpikg.mpg.de> wrote:
>
>> No it did not work. When I am generating 123 units its all ok. If I am
>> adding just one unit more everything breaks.
>> with the following error. Have no idea what to do next. Any help will be
>> appreciated.
>>
>
> I don't think it's that common to use the sequence command like this (I
> certainly don't build anything more than ~10 residues with it). One idea
> is to build up 120-residue chunks:
>
> chunk1 = sequence {RES1 RES2 RES3 ... RES120}
> chunk2 = sequence {RES121 RES122 ... RES
>
> 240}
> ...
> system = sequence {chunk1 chunk2 ...}
>
> This can recurse as long as is necessary to build the whole system. I'm
> not sure if the resulting chunk# units remember their "head" and "tail"
> designation (i.e., if tleap will know how to connect chunk1 and chunk2, for
> instance), but it's at least worth a shot.
>
> If that doesn't work, my next idea would be to grep for the 124 limit that
> you found in the .m4 file and see if it appears to be hard-coded in other
> places as well.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jan 05 2016 - 11:30:03 PST
