I try to create the input for MMPBSA.py but It seems it does not
recognize my mask
This is my input:
Pairwise GB and PB decomposition
&general
ligand_mask= :311-482,
receptor_mask= :1-310,483-484,
startframe=3000, endframe=5000, interval=10, verbose=1,
/
&gb
igb=5, saltcon=0.100,
/
&pb
istrng=0.100,
/
&decomp
idecomp=1,
dec_verbose=0,
/
This is the error:
Warning: Input error! "483-484" is not recognized. Initialize variables
with "="
Thanks
Chiara
On Thu, 2012-09-13 at 11:17 -0400, Jason Swails wrote:
> On Thu, Sep 13, 2012 at 11:00 AM, Chiara Pallara <chiara.pallara.bsc.es>wrote:
>
> > Thanks very much.
> > Sorry for the mistake, Actually, I'm trying to use mm_pbsa.pl.
> > In the .DECOMP section of the input, I have to set the receptor and
> > ligand residues.
> > I don't know how I can set, as receptor, the residues from 1 to 310 and
> > from 482 to 483 (2 ions of Mg2+).
> > Can You help me?
> > Chiara
> >
>
> If you try using MMPBSA.py, this mask will be determined automatically (the
> only requirement to automatic mask determination is that the ligand
> residues appear continuously inside the complex -- receptor residues do not
> have to be continuous). This should simplify the input file.
>
> Since I don't have much experience with the perl version, my suggestion is
> to look at some of the example files and try to adapt them to your system
> until someone more knowledgeable is able to respond if you don't want to
> use MMPBSA.py.
>
> HTH,
> Jason
>
WARNING / LEGAL TEXT: This message is intended only for the use of the
individual or entity to which it is addressed and may contain
information which is privileged, confidential, proprietary, or exempt
from disclosure under applicable law. If you are not the intended
recipient or the person responsible for delivering the message to the
intended recipient, you are strictly prohibited from disclosing,
distributing, copying, or in any way using this message. If you have
received this communication in error, please notify the sender and
destroy and delete any copies you may have received.
http://www.bsc.es/disclaimer
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 13 2012 - 09:00:04 PDT
