Quoting Sergey Samsonov <sergeys.biotec.tu-dresden.de>:
> I just tried to follow the examples with already prepared files from
> the web tutorial which I have all in the same directory.
> After I start perl RED-vIII.pl
> ---------------------------
> * Welcome to R.E.D. III *
> RESP ESP charge Derive
> http://q4md-forcefieldtools.org/RED/
>
> CHARGE TYPE = RESP-A1
> ---------------------------
> ERROR: The initial P2N file can not be found
R.E.D. needs Mol_red$n.p2n files to run...
For instance:
- If $n = 1 (This is a single molecule fitting approach), you only
need to provide Mol_red1.p2n (the name being fixed)...
- If $n = 3 (This is a three molecule charge fitting approach), you
need to provide three p2n files: Mol_red1.p2n, Mol_red2.p2n and
Mol_red3.p2n.
- Now, if you provide Mol_red1.p2n, Mol_red2.p2n and Mol_red4.p2n,
R.E.D. will only use the 2 first p2n files since you have a hole in
the list of p2n files.
> Do you think there could be any problems with RED because I use
> AMBER8.0 and not AMBER9.0 version?
No
Before running R.E.D. it is always a good idea to check if the program
binaries interfaced by R.E.D. are found: i.e. using the UNIX commands:
which resp
which g98 (if you use Gaussian, 1998 for instance); or which g03
> At the same time when I do test/antechamper/Run_tp_resp I get this:
>
> Running: $AMBERHOME/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
> ANTECHAMBER_BOND_TYPE.AC -f ac -j full
> Running: $AMBERHOME/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
> Running: $AMBERHOME/exe/espgen -o ANTECHAMBER.ESP -i tp.log
> Running: $AMBERHOME/exe/respgen -i ANTECHAMBER_RESP.AC -o
> ANTECHAMBER_RESP1.IN -f resp1
> Running: $AMBERHOME/exe/respgen -i ANTECHAMBER_RESP.AC -o
> ANTECHAMBER_RESP2.IN -f resp2
> Running: resp -O -i ANTECHAMBER_RESP1.IN -o ANTECHAMBER_RESP1.OUT -e
> ANTECHAMBER.ESP -t qout
> Amber8 Module: resp
> forrtl: severe (24): end-of-file during read, unit 5, file
> /home/bioinfp/sergeys/AmberMy/RESP/Test/ANTECHAMBER_RESP1.IN
> Image PC Routine Line Source
> resp 080A5A5A Unknown Unknown Unknown
> resp 080A48B9 Unknown Unknown Unknown
> resp 08085E45 Unknown Unknown Unknown
> resp 0805C58E Unknown Unknown Unknown
> resp 0805C2BE Unknown Unknown Unknown
> resp 0806A01C Unknown Unknown Unknown
> resp 08049F79 Unknown Unknown Unknown
> resp 08049DA9 Unknown Unknown Unknown
> resp 08049C35 Unknown Unknown Unknown
> libc.so.6 003A0DE3 Unknown Unknown Unknown
> resp 08049B71 Unknown Unknown Unknown
> resp -O -i ANTECHAMBER_RESP2.IN -o ANTECHAMBER_RESP2.OUT -e
> ANTECHAMBER.ESP -q qout -t QOUT
Sorry, I do not know very well antechamber. Can you execute resp in a
standalone way ? i.e. "without antechamber" using the command just
above printed by antechamber:
resp -O -i ANTECHAMBER_RESP2.IN -o ANTECHAMBER_RESP2.OUT -e
ANTECHAMBER.ESP -q qout -t QOUT
-i is the RESP input
-o is the RESP output
-e is the MEP coming from Gaussian converted to the RESP format
here you do not have the punch file (-p) ... ?
Below, are aliases to run resp in a standalone way; i.e. without
antechamber or without R.E.D.:
alias resp1 'resp -O -i input1 -e espot -o output1 -p punch1 -q qout
-t qout1 -w qwts -s esout1'
alias resp2 'resp -O -i input2 -e espot -o output2 -p punch2 -q qout1
-t qout2 -w qwts -s esout2'
regards, Francois
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Received on Sun Jul 22 2007 - 06:07:10 PDT
