I have some success :)
I've loaded my structure to xleap by this
source leaprc.ff10
m = loadpdb 1mag.pdb
edit m
so now I wounder to know some detailes about this run
I have small protein wich consist of 2 identical allpha helices
1- First of all I just want to make some editions on this initial
structure. i dont want to create any amber topology. So I just want to
obtain a processed pdb file as output.
How I can add some ceping groups? What should I do to save only my
processed pdbs? ( in some tutorials I've found how to save topologies etc-
i dont want do it now )
E.g for this exersice I'd like to build CAP groups on N and C termii of
each chain of my protein.
2- What xleap force field should I use for such parametrisation? My protein
consist of some non-standart amino-acids ( D- isomers) like D-leucyn and
D-valine. What leap force field already has parametrisation for such
aminoacids?
Also I want to perform further simulation ig Gromacs for instance so I'm
looking for a force field wich could be best compatible with some gromacs
force fields like gromos etc
James
2011/11/1 James Starlight <jmsstarlight.gmail.com>
> I'm using xleap with graphical interphase so I've load pdb just from
> graphical option Load pdb :)
>
> May be it could be helpfull- when xleap or tleap loaded I obtained that
>
> Welcome to LEaP!
> (no leaprc in search path)
>
> besides I've problem with variables of all amber programs.
> before installation I've define path and set environment but after
> installation in new terminal window I must to define path again.
> Is there any way to define path for ambertools permamentary?
>
> Thanks
>
> James
>
> 2011/11/1 Pavan Giovanni <giovanni.pavan.supsi.ch>
>
>> Hi,
>> just to be sure I was clear...
>> I suppose you load your pdb into leap using the command:
>>
>> $AMBERHOME/bin/tleap -f tleap.in
>>
>> where in your tleap.in file you have the command
>>
>> a=loadpdb x.pdb
>>
>> written inside, right?
>> what happens to me quite often is that the file "tleap.in"
>> itself become unreadable (and you receive "sintax error"
>> messages)...not the .pdb file.
>> so you could try to edit your tleap.in file in linux and
>> just "add a space and remove the space and save"...after
>> that it should work.
>> if this is not useful for you, I am sorry but I don't
>> think I can be useful in any manner... :-(
>> just try
>> bye
>> giovanni
>>
>> On Tue, 1 Nov 2011 15:17:38 +0400
>> James Starlight <jmsstarlight.gmail.com> wrote:
>> > Pavan, hello!
>> >
>> > I've already tried to do that but it didnt work :(
>> > I could not load any pdb's (even from example subdir
>> >from amber tools)
>> >
>> > James
>> >
>> > 2011/11/1 Pavan Giovanni <giovanni.pavan.supsi.ch>
>> >
>> >> Dear James,
>> >> this happened to me quite often...it could be a
>> >>formatting
>> >> error if you have modified the file in Windows and then
>> >> you move it in linux via ssh or scp.
>> >> just try to do that:
>> >> edit the file in linux, make any modification (write a
>> >> letter and delete it) and save again the file in linux.
>> >> It should work.
>> >> bye
>> >> giovanni
>> >>
>> >> On Tue, 1 Nov 2011 03:44:07 -0700
>> >> James Starlight <jmsstarlight.gmail.com> wrote:
>> >> > Dear Amber Users!
>> >> >
>> >> > I have some problem with loading pdb files in the
>> >>XLEAP
>> >> >software.
>> >> >
>> >> > I've tried to load different pdb files but in any
>> >>cases
>> >> >I've obtained
>> >> > ERROR: Syntax error
>> >> >
>> >> > What I've done wrong ?
>> >> >
>> >> > James
>> >> > _______________________________________________
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>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
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Received on Tue Nov 01 2011 - 06:30:03 PDT
