[Chimera-users] Chimera vs Amber, which one digresses from the average pdb rules?

[Francesco Pietra]

--- Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Francesco,
> In Chimera we have worked to create PDB files in the correct format,  
> as described at the PDB web site:
> http://www.wwpdb.org/docs.html
> 
> We also have a brief intro to this format in the Chimera documentation:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
> framepdbintro.html
> 
> We decided the best approach would be to follow the format standard,  
> including recent changes. However, lots of other programs don't  
> follow the standard, and when using multiple programs it is usually  
> necessary to hand-edit or use scripts to convert files.
> 
> In version 2.3 PDB format, the atom name occupies columns 13-16 with  
> the element symbol right-justified in 13-14.  So if the element  
> symbol is one character, it is supposed to be in column 14, not 13, i.e.
> C315 should be 5C31.  The output you are getting follows this role.
> 
> In version 3.0 PDB format, that is still true, except for hydrogen  
> atoms.

Here I really don't understand. With your "including recent changes" above, I
understand that you follow 3.0 or 3.1 PDB format. Unless you add that 3.0 and
3.1 formats are exercises not to follow (the official pdb booklet I have, is V.
2.3, added of V. 3.0 and V 3.1). If you follow 3.0, modification of Amber's
file

ATOM    531 H15X POPC    4     -41.330 -15.752   3.099  1.00  0.00      L11  H
ATOM    532 H15Y POPC    4     -40.694 -14.148   3.019  1.00  0.00      L11  H
ATOM    533 C316 POPC    4     -39.787 -15.573   1.664  1.00  0.00      L11  C
ATOM    534 H16X POPC    4     -39.553 -16.661   1.544  1.00  0.00      L11  H
ATOM    535 H16Y POPC    4     -40.534 -15.211   0.948  1.00  0.00      L11  H
ATOM    536 H16Z POPC    4     -38.782 -15.094   1.533  1.00  0.00      L11  H
TER

by Chimera, as follows (as it happened to me, see previous mail):

HETATM  129 XH15 POPC    1     -40.149 -41.259   3.406  1.00  0.00           H
HETATM  130 YH15 POPC    1     -39.107 -42.686   3.702  1.00  0.00           H
HETATM  131 6C31 POPC    1     -40.650 -42.850   2.121  1.00  0.00           C
HETATM  132 XH16 POPC    1     -41.411 -42.165   1.778  1.00  0.00           H
HETATM  133 YH16 POPC    1     -39.859 -42.645   1.328  1.00  0.00           H
HETATM  134 ZH16 POPC    1     -40.899 -43.957   2.212  1.00  0.00           H 

breaks the H rules.

Finally, everything in the "classic" are is in view of MD. Even DOCK is
recommended as a preliminary to MD (by both Scott Brozell and D case).
Therefore, it is a pity - to say politely - having to spend so much effort in
rectifying files from pre-programs. Unless Chimera is bound to some other MD
suite than Amber, to which MD suite Chimera's files flow in without barriers.

This is under my sincere assertion that I consider Chimera a gem. The gift of a
gem. And it is far from me to try to engage in discussion on matter not of my
competence, like these ones.

My only aim is: once TERs are inserted, as I did, I have "simply" to
recondition the files for the position of single-character elements (including
H). This is what I'll try, allowing for an European night of break to see if
contrary suggestions come out. Lot of users should have had similar problems.

Thanks a lot
Francesco

> 
> Both versions follow the HETATM/ATOM rules I mentioned earlier.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> 
> 
> 



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