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 ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs