I ran ambpdb with -bres flag, but it doesn't generate chain id which the
Leview expects (since it is present even in pdb with only one chain). I
will try sed/awk to insert chain id and see if it fixes the problem.
My intention here is to be able to generate gif animation by combining many
images (derived from MD trajectories via pdb files) like the one I attached
earlier.
This will give a focused view on which residues come within interaction
distance without having to load the whole trajectory or look/analyze into
text files generated by cpptraj. I hope that makes sense to you (and others
on the list).
Below is the example where Leview works to rcsb file, but fails to
recognize files generated by pdb (in this case probably because it lacks
chain id information).
C:\Users\r11831vd\Downloads\LeViewLine2.0\LeViewLine>java -jar
LeViewLine.jar 2prg -r 1 1 A -flat
downloading 2prg PDB entry
C:\Users\r11831vd\Downloads\LeViewLine2.0\LeViewLine>java -jar
LeViewLine.jar leview-test.pdb -r 473 473 -flat
Exception in thread "main" java.lang.StringIndexOutOfBoundsException:
String index out of range: 30
at java.lang.String.charAt(Unknown Source)
at File2.getMolecule(File2.java:445)
at LeView.main(LeView.java:323)
C:\Users\r11831vd\Downloads\LeViewLine2.0\LeViewLine>
On Tue, Jun 4, 2019 at 1:11 PM David A Case <david.case.rutgers.edu> wrote:
> On Tue, Jun 04, 2019, Vaibhav Dixit wrote:
>
> >I noticed that there are (small) differences in PDB file formats between
> >RCSB and AMBER.
>
> You don't say what you mean by "AMBER". [Using ambpdb gets a PDB-format
> file that follows closely the wwPDB standard. Use the "-bres" option to
> get standard residue names. Residue numbers and chainID's tend to get
> lost when running Amber simulations, but these can be retrieved via
> add_pdb and the "-ext" option to ambpdb.]
>
> You also don't say what differences you find, or what specific
> problems LeVIew has.
>
> >LeView 2D interaction map
>
> The hbond command in cpptraj reports on hydrogen bonds. The "closest"
> command can provide contact information between the ligand and receptor.
> But, by all means, Use LeView if it suits your needs.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 04 2019 - 06:30:03 PDT
