All:
I'm trying to generate force field parms for a molecule that contains
Zn(II) coordinated to a porphyrin. It also has a number of phenyls
attached for a total of about 269 atoms. I run antechamber with the
following command line:
antechamber -i ZnPJ22.log -fi gout -o zpj.prepc -fo prepc -c resp -rn
ZPJ -at amber
and get the messages shown below (note, I did increase the maxatom and
maxbond parms in define.h and recompiled with all antechamber bugfixxes
to handle the number of atoms in the system). Now part of the problem,
I think, is that antechamber doesn't understand Zn. How are the
requisite parms established for APS.DAT (but then do other files have to
be modified too eg RADIUS.DAT, looks like metals are 2.0...regardless,
but I'm not sure what this refers to). So, I'm guessing (hoping), given
the and/or at the end of 1, 2, and 3, this may fix things if I can
figure out how to modify the APS.DAT, etc.
Then there is all the stuff after (3) which I don't understand at all.
I can't find MAXPATHATOMNUM in define.f, other files. Perhaps this will
go away once 1 or 2 or 3 are taken care of?
Can anyone help me out with this? Thank.
Pete
For atom[2]:Zn1, the best APS is not zero, exit
Cannot successfully assign bond type for this molecule, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
The number of the path atoms exceeds MAXPATHATOMNUM(10000) for
atom[0],extend the size and reallocate the memory
The number of the path atoms exceeds MAXPATHATOMNUM(15000) for
atom[0],extend the size and reallocate the memory
The number of the path atoms exceeds MAXPATHATOMNUM(20000) for
atom[0],extend the size and reallocate the memory
The number of the path atoms exceeds MAXPATHATOMNUM(10000) for
atom[2],extend the size and reallocate the memory
The number of the path atoms exceeds MAXPATHATOMNUM(15000) for
atom[2],extend the size and reallocate the memory
The number of the path atoms exceeds MAXPATHATOMNUM(20000) for
atom[2],extend the size and reallocate the memory
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Jun 30 2005 - 20:53:01 PDT
