AMBER Archive (2004)

Subject: RE: AMBER: problem loading pdb in leap.

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Aug 24 2004 - 12:35:08 CDT

Dear Anshul,

There are a couple of problems I found with the pdb file you sent me. First
of all it is in DOS format with carriage returns and line feeds, seen as ^M
when you edit in vi. This should not cause a problem in xleap but can cause
problems in some programs on unix. If you are using linux you can use the
command "dos2unix" to convert a dos format text file to a unix format.

The second problem and the one that I suspect is causing the problem is the
misallignment of the residue number. Your file has:

ATOM 1 CQ LYK 1 15.617 -10.349 -5.935 1.00 0.00
C
ATOM 2 NC LYK 1 15.557 -9.508 -7.005 1.00 0.00
N
ATOM 3 C LYK 1 16.266 -9.939 -8.126 1.00 0.00
C
ATOM 4 N LYK 1 16.953 -11.142 -8.203 1.00 0.00
N
ATOM 5 C1 LYK 1 16.910 -11.920 -7.054 1.00 0.00
C

This has one too many spaces between the LYK and the 1 and so does not
conform to the pdb standard. This is why both xleap and VMD fail to load it
correctly. If you convert it to:

ATOM 1 CQ LYK 1 15.617 -10.349 -5.935 1.00 0.00
C
ATOM 2 NC LYK 1 15.557 -9.508 -7.005 1.00 0.00
N
ATOM 3 C LYK 1 16.266 -9.939 -8.126 1.00 0.00
C
ATOM 4 N LYK 1 16.953 -11.142 -8.203 1.00 0.00
N
ATOM 5 C1 LYK 1 16.910 -11.920 -7.054 1.00 0.00
C

By deleting a space after the residue name through the entire file the
problems seem to go away. I only tried this with a small fragment of your
pdb file but I suspect that is the problem. To do this manually will take
you a long time. There may be some programs that will detect this problem
and fix it. Antechamber might work. I didn't try it.

I hope this helps.
All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of anshul_at_imtech.res.in
> Sent: 24 August 2004 09:35
> To: amber_at_scripps.edu
> Subject: RE: AMBER: problem loading pdb in leap.
>
> Dear Ross,
> Please find attached the pdb file for the modified protein.
> waiting for your expert comments.
> Regards,
>
> Anshul Awasthi
> Bioinformatics Center
> Institute of Microbial Technology
> Chandigarh, India.
> Mobile +91-9872220352
>
>

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