On Wed, Jul 16, 2014 at 9:41 AM, Valentina Romano <
valentina.romano.unibas.ch> wrote:
> Dear Amber users
>
> I I want to run a MD of a kinase in complex with ATP.
> To build ATP parameters I used files .frcmod and .prep found on
> http://www.pharmacy.manchester.ac.uk/bryce/amber/ and I loaded them in
> tleap.
>
> I used the following script:
>
> source leaprc.ff99SB
> loadamberparams ATPphos.frcmod
> loadamberprpe ATP.prep
> ATP = loadpdb ATP.pdb
> saveoff ATP ATP.lib
> saveamberparm ATP ATP.prmtop ATP.inpcrd
> quit
>
> I got the following error:
>
> Loading parameters: ./ATPphos.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> # Modifications to the AMBER94 force field for polyphosphates
>
This indicates that your frcmod was read.
>
> ERROR: syntax error
>
This suggests a problem with your very next command. Looking at that
command, loadAmberPrep is misspelled (loadamberprpe), leading to the syntax
error. Another strategy to debugging this kind of problem is to load up
tleap and enter the commands one-by-one, copying and pasting the commands
from your script. Had you done this, you would have hopefully noticed the
misspelling, but certainly would have noticed that it was the loadAmberPrep
command that failed.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 16 2014 - 10:00:03 PDT
