Re: [AMBER] Error while running antechamber for modified amino acid residue

From: Rajarshi Roy <phd1701171011.iiti.ac.in>
Date: Sun, 27 Aug 2017 21:52:33 +0530

Hi ,
I attached my CRO.cif. Here I deleted "_chem_comp.type "L-PEPTIDE
LINKING" this line, because
 previously I was getting
/apps/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Residue (CRO) has a type of LINKING.
while running of the downloaded CRO.cif via antechamber.


On Sun, Aug 27, 2017 at 6:27 PM, David A Case <david.case.rutgers.edu>
wrote:

> On Sun, Aug 27, 2017, Rajarshi Roy wrote:
>
> > I have to create lib file for a modified amino acid residue. For that I
> am
> > trying to run the code of *tutorial B5 ("Simulating the Green
> > Fluorescent **Protein")
> > but i am getting this following error.*
> >
> >
> > *antechamber -fi ccif -i CRO.cif -bk CRO -fo ac -o cro.ac
> > -c bcc -at amber
>
> > Welcome to antechamber: molecular input file
> > processor.acdoctor mode is on: check and diagnosis problems in the input
> > file.antechamber: mmcif.c:70: rmmcif: Assertion `col2 >= 0'
> failed.Aborted
> > (core dumped)*
>
> Can you post your CRO.cif file? The code is looking to see if this is a
> LINKING type residue, but cannot find a "type" column.
>
> When I extract the CRO.cif file from components.cif, I don't see the error
> you report.
>
> You could also try commenting out the block starting at line 68
> of mmcif.c (in AmberTools/src/antechamber) that exits for linking residues.
> Type "make install" in that directory, then re-run you job.
>
> I think we need to add a flag that allows LINKING residues to be processed.
>
> ....dac
>
>
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>



-- 
with regards
Rajarshi Roy
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India



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Received on Sun Aug 27 2017 - 09:30:02 PDT
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