Dear Sook Wong,
> I am trying to generate the parameters for attached PDB without
> success as my command line is showing below:
>
> FATAL: Atom .R<POT 4875>.A<POT 1> does not have a type.
> FATAL: Atom .R<POT 4876>.A<POT 1> does not have a type.
> FATAL: Atom .R<CLA 4877>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4878>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4879>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4880>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4881>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4882>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4883>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4884>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4885>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4886>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4887>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4888>.A<CLA 1> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> Can anyone explain how to resolve this problem? Appreciated.
If you use PyRED at R.E.D. Server Dev.
http://q4md-forcefieldtools.org/REDServer-Development/ an entire force
field (FF) is generated for the input molecules and a LEaP script is
created allowing the user to directly use the generated FF.
see a simple case at: http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
for instance:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#6
tar -jxvf P$x.tar.bz2
cd P$x/Data-R.E.D.Server/Data-Default-Proj
xleap -f leaprc.q4mdfft
all the commands available in this LEaP script has an Amber reference
to the html documentation; i.e.
http://ambermd.org/doc6/leap.html
thus any user has a direct access to the web page for each LEaP command...
an atom type has to be declared before to be loaded...
regards, Francois
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Received on Thu Apr 09 2015 - 00:30:02 PDT
