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

[Francesco Pietra]

A lipid/water pdb file that was good for Leap (Amber9) to get top/crd, once
passed through Chimera 2470 to remove residues is no more good for Leap.

All TER were removed by Chimera, ATOM renamed HETATM, while CONECT records
were added.

As such, Leap said:
In file [chirality.c], line 142
Atom named C217 from POP did not match
Aborting

I knew such type of message. There is no C217 atom. On previous (different)
occasions, insertion of TER records put the house in order.

I inserted all TERs between POPC residues and between WAT residues (thanks to
Python!).

Now Leap said:
In file [atom.c], line 444
bond AtomProblem found
Aborting

As I did not know this type of message, I tried to investigate that line 444.
Following vim's command

:n,444

that line, indicated at bottom of terminal as "444,1", reads

HETATM  441  O31 POPC    5     -44.082 -12.831  14.685  1.00  0.00           O


A carbon atom (if "[atom.c]" means carbon, is at line 447,1, which reads

HETATM  444  C32 POPC    5     -46.343 -12.925  15.140  1.00  0.00           C


In the original (good for Leap) pdb those lines read:

ATOM    441  O31 POPC    4     -37.722 -19.453  18.019  1.00  0.00      L11  O

ATOM    444  C32 POPC    4     -39.844 -19.273  18.941  1.00  0.00      L11  C


Chimera also changed atom names, such as in the final part of the POPC
residue (Sybyl naming?, if so, there is an alternative in Chimera not to follow
Sybyl rules?)

HETATM  528 XH14 POPC    5     -47.646  -9.424  -0.112  1.00  0.00           H
HETATM  529 YH14 POPC    5     -46.217 -10.553  -0.172  1.00  0.00           H
HETATM  530 5C31 POPC    5     -47.890 -11.168  -1.419  1.00  0.00           C
HETATM  531 XH15 POPC    5     -47.763 -12.309  -1.296  1.00  0.00           H
HETATM  532 YH15 POPC    5     -48.986 -11.063  -1.417  1.00  0.00           H
HETATM  533 6C31 POPC    5     -47.242 -10.566  -2.756  1.00  0.00           C
HETATM  534 XH16 POPC    5     -46.135 -10.759  -2.831  1.00  0.00           H
HETATM  535 YH16 POPC    5     -47.802 -11.112  -3.597  1.00  0.00           H
HETATM  536 ZH16 POPC    5     -47.451  -9.454  -2.737  1.00  0.00           H
TER


which, in the original (good) pdb was:

ATOM    528 H14X POPC    4     -38.665 -14.879   4.398  1.00  0.00      L11  H
ATOM    529 H14Y POPC    4     -39.080 -16.603   3.952  1.00  0.00      L11  H
ATOM    530 C315 POPC    4     -40.370 -15.221   2.996  1.00  0.00      L11  C
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

Although it is not clear to me yet where really Leap crashed (nor am I placing
Leap as the standard; simply I have to get top/crd from it, if I want to carry
out MD with Amber). Elaine already kindly clarified the ATOM/HETATM issue. I
hope now to get help about the atom names , ie a table of conversion to get
Leap working or a not-Sybyl choice in Chimera.

Once again, I regret very much to pose so many problems of language.

Thanks
francesco pietra 


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