just realized that tleap writes pdb file even (more) differently.
It doesn't write the last column for atom identifiers.
Most of the visualization and ambertools don't seem to have problem with
this, but I'm sure ambertools generated pdb files are far-way from the rcsb
format given here
<
http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html>
and here
<
http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM>
for example.
Pasted below are typical heads of pdb files generated by tleap and ambpdb
respectively.
Any confirmation/clarification from developers and experts will be highly
appreciated.
Are there different pdb formats being used by different software
developers? (leaving some columns empty e.g. chainid here, isn't it like
not following the universal pdb format?)
I hope somebody is reading and interested in this.
thanks in advance.
tleap generated pdb missing the chain identifiers, and importantly last
coloumn for atom identifiers:
ATOM 1 N GLY 1 73.178 108.167 13.451 1.00 0.00
ATOM 2 H1 GLY 1 72.728 108.901 13.978 1.00 0.00
ATOM 3 H2 GLY 1 72.780 108.143 12.523 1.00 0.00
ATOM 4 H3 GLY 1 74.178 108.248 13.570 1.00 0.00
ATOM 5 CA GLY 1 72.815 106.872 14.065 1.00 0.00
ATOM 6 HA2 GLY 1 72.300 106.257 13.327 1.00 0.00
ATOM 7 HA3 GLY 1 73.722 106.363 14.392 1.00 0.00
ATOM 8 C GLY 1 71.917 107.073 15.244 1.00 0.00
ATOM 9 O GLY 1 71.494 106.120 15.890 1.00 0.00
ATOM 10 N THR 2 71.738 108.340 15.641 1.00 0.00
ambpdb generated pdb file missing the chain identifiers:
ATOM 1 N GLY 1 73.178 108.167 13.451 1.00 0.00
N
ATOM 2 H1 GLY 1 72.728 108.901 13.978 1.00 0.00
H
ATOM 3 H2 GLY 1 72.780 108.143 12.523 1.00 0.00
H
ATOM 4 H3 GLY 1 74.178 108.248 13.570 1.00 0.00
H
ATOM 5 CA GLY 1 72.815 106.872 14.065 1.00 0.00
C
ATOM 6 HA2 GLY 1 72.300 106.257 13.327 1.00 0.00
H
ATOM 7 HA3 GLY 1 73.722 106.363 14.392 1.00 0.00
H
ATOM 8 C GLY 1 71.917 107.073 15.244 1.00 0.00
C
ATOM 9 O GLY 1 71.494 106.120 15.890 1.00 0.00
O
ATOM 10 N THR 2 71.738 108.340 15.641 1.00 0.00
N
On Wed, Jun 19, 2019 at 2:11 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Dear All,
> Am happy to share that I wrote a script to convert ambpdb pdb files into
> RCSB-formatted files which LeView is recognizing and generating useful
> (beautiful) 2D graphs of ligand-receptor interactions.
> Example image generated from sustiva tutorial prmtop inpcrd files is
> attached.
> The script is taking 5min 8sec on a protein with 543 residues and thus I
> think is not an optimum code, but does the job.
> I believe one can use this to generate 2D picture from MD trajectories and
> combine them into a cartoon animation (gif) of the MD simulation.
> Please let me know if anyone is interested in utilizing this script along
> with LeView.
> FYI - LeView authors are cc'd (thanks to them for helping me fix the
> errors that LeView reports with ambpdb generated pdb files).
> Prof. Case, thanks for your valuable comments/suggestions on this and
> other topics.
> best regards
>
>
> On Tue, Jun 4, 2019 at 2:12 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
>
>> 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
>>
>>
>
> --
>
> 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
>
>
--
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
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Received on Wed Jun 19 2019 - 15:00:02 PDT
