On Mon, Feb 24, 2014 at 12:23 PM, nalini chauhan <nalinichauhan.05.gmail.com
> wrote:
> Respected Sir,
>
> I am working on MCPB and trying to get charge on my protein linked with
> zinc ion. While running PROTEIN_sidechain.bcl file, I am getting this
> error while building the cluster. Here I am attaching my pdb and .bcl file
> and kindly look into it and help me out
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: selection::parse ###
> ### Message: selection string = /PROTEIN/CLR/HE1
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: selection::parse ###
> ### Message: selection string = /PROTEIN/1/HIE-65
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: selection::parse ###
> ### Message: Can't find: HIE-65 in molecule: PROTEIN_fixed /col/mol/smol
> selection error (4)
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: MCPB::addToResidue ###
> ### Message: Error in selection parsing
> ### ### ### ###
>
It seems that the selection strings you're using in your .bcl file is not
being recognized. I cannot actually see any of these selection strings in
use, which leads me to believe the problem is actually occurring in the
file PROTEIN_settings.bcl (which is sourced by the PROTEIN_sidechain.bcl
file you attached to your email).
My guess is that you were supposed to change those selection strings for
your system but did not. You should consult the MTK++ manual (in
$AMBERHOME/doc) for documentation regarding the syntax of the selection
strings (page 12) and the MCPB program (chapter 12 and section 15.10).
It may also help to download the MCPB examples (look for the MTKPP_Examples
file under the "Downloads" section of the Amber website) and look at those
if you haven't already. This is all the help that I, personally, can
provide since I've never (successfully) used MCPB before (I tried for an
afternoon once several years ago, but didn't get too far).
These programs have not been actively developed for some time and those
experienced with the code do not monitor this list very often anymore as
far as I can tell. As a result, you are unlikely to get as much support
using this program as you will with other programs in AmberTools.
Experimenting, studying the relevant parts of the MTK++ manual, and the
aforementioned examples will hopefully help you use this software, and you
should check at every step that the results you get seem reasonable.
This last part (about checking) is good advice in general for metal center
parameter building. Such parameter sets are very difficult to derive, and
while MCPB handles some of the heavy lifting it is a nearly impossible task
to automate.
If you choose to continue with MCPB and MTK++, I would expect the first
system you use it on will take a lot of time to learn how to use this
program. It may well prove worthwhile if you need to do this with many
different systems. There are alternative choices for deriving parameters,
such as R.E.D. for the charge derivation and potentially paramfit for the
parameter fitting but my experience with these programs is limited as well.
It might be worth looking at various references that worked on similar
systems to see how they parametrized their systems...
Hope this helps,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Feb 24 2014 - 18:30:03 PST
