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 - 12:30:02 PDT
