Hi Ben,
I've faced with the problem loading scripts from membrane tutorial.
Initially all scripts have been placed to
$AMBERHOME/AmberTools/src/etc
and corresponded path have been added to /etc/bash.bashrc
now all scripts from /etc/ works fine but not two recently scripts from
tutorial
own.starlight ~/Desktop/Amber/tutorials/membrane $ charmmlipid2amber.py -i
b2ar_charm.pdb -c
$AMBERHOME/AmberTools/src/etc/charmmlipid2amber/charmmlipid2amber.csv -o
b2ar_amber.pdb
bash: ./charmmlipid2amber.py: PYTHONEXE: bad interpreter: No such file or
directory
own.starlight ~/Desktop/Amber/tutorials/membrane $ cpinutil.py
CpinInputError: prmtop file (prmtop) is missing
own.starlight ~/Desktop/Amber/tutorials/membrane $ vmd_box_dims.sh
bash: /home/own/amber14/AmberTools/src/etc/vmd_box_dims.sh: /bin/bash^M:
bad interpreter: No such file or directory
Does it some problem with my bash or something else ?
James
2014-06-09 23:02 GMT+04:00 Benjamin D Madej <bmadej.ucsd.edu>:
> Hi James,
>
> Sorry about the problem with charmmlipid2amber.py. It was a problem with
> residue numbering. I am currently working on getting the fix out to all
> users.
>
> Here is an updated version of the script for you to use now:
> https://dl.dropboxusercontent.com/u/26203202/charmmlipid2amber.tar.bz2
>
> As for your protein system, it appears that that LEaP may be trying to
> connect a lipid molecule and a protein molecule. Make sure that you have
> appropriate TER cards in your structure. For example, the protein chains
> must be ended with a TER card and the lipids should follow the Lipid14 PDB
> format.
>
> All the best,
> Ben Madej
> UCSD Chemistry and Biochemistry
> SDSC
>
> ________________________________________
> From: James Starlight [jmsstarlight.gmail.com]
> Sent: Friday, June 06, 2014 9:26 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] charmmlipid2amber.py
>
> also below error have been appeared during processing of the rhodopsin by
> tleap wih he same membrane (this time I had no problem with the conversion
> of charm to amber pdb in comparison to the above case) using rhodopsin from
> the tutorial.
>
> input
>
> source leaprc.ff12SB
> source leaprc.lipid14
> m = loadpdb rho_amber.pdb
> #check m
> saveamberparm m rhodopsin.prmtop rhodopsin.inpcrd
>
>
> output
>
>
> .R<PA 349>.A<C13 41>,
> .R<ALA 348>.A<C 9>,
> .R<PA 349>.A<H2R 45>, and
> .R<PA 349>.A<H2S 46>
> to atoms
> .R<PA 349>.A<C13 41>,
> .R<PC 1>.A<C11 5>,
> .R<PA 349>.A<H2R 45>, and
> .R<ALA 348>.A<C 9>
> This error may be due to faulty Connection atoms.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 142
> !FATAL: Message: Atom named C11 from PC did not match !
> !
>
>
>
> 2014-06-06 16:40 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
>
> > Dear Amber's users!
> >
> >
> > I have a problem in the conversion charm gui PDB to amber PDB
> >
> > charmmlipid2amber.py -i b2ar_charm.pdb -c
> > $AMBERHOME/AmberTools/src/etc/charmmlipid2amber/charmmlipid2amber.csv -o
> > b2ar_amber.pdb
> > Error: Number of atoms in residue does not match number of atoms in
> > residue in replacement data file
> >
> >
> > here you can find my pdb
> > http://www.charmm-gui.org/?doc=input/membrane&time=1402044938
> >
> > I suppose this is some bud isn't it?
> >
> >
> > TFH
> >
> > James
> >
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Received on Mon Jun 09 2014 - 12:30:03 PDT
