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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 05 2016 - 10:30:03 PST
