I have being able to test successfully some MD files from Amber using 11.7.1 It works very well. I will post the example soon --it may well be run across the web, as the 4 files sum 1.5MB gzipped, or at least serve as test files for the collection.
However, I am havign a little problem that seems related to the Amber reader. This file has a GTP, with P atoms named PA, PB, PG. Jmol is reading the latter two as lead and protactinium, and drawing too many (long) bonds from them. First I thought it would be a text misaligning issue, but after looking at the topology file I see that there are no columns, just 4-character chunks, and atoms as HE, NE, CA are not being misinterpreted (that is, they are correctly read as hydrogen, nitrogen, carbon). Is there a chance to recognize and fix the problem? I can send the file offlist if needed. I think that the file comes from Amber itself, but I need to double check that with the person that did the work, as well as the AMber version if it is meaningful. This is a portion of the file contents: %FORMAT(20a4) HH31CH3 HH32HH33C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O N H CA HA CB HB2 HB3 OG HG C O N H CH3 HH31HH32HH33HH31CH3 HH32HH33C O N H CA HA CB HB CG2 HG21HG22 HG23OG1 HG1 C O N H CH3 HH31HH32HH33HH31CH3 HH32HH33C O N H CA HA2 HA3 C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 NE2 HE21HE22C O N H CH3 HH31HH32HH33HH31CH3 HH32HH33C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 NE HE CZ NH1 HH11HH12NH2 HH21HH22C O N H CH3 HH31HH32HH33H1 O H2 O3G PG O1G O2G O3B PB O1B O2B O3A PA O1A O2A O5* C5* H5*1H5*2C4* H4* O4* C3* H3* O3* HO*3C2* H2* O2* HO*2C1* H1* N9 C8 H8 N7 C5 C6 O6 N1 H1 C2 N2 H21 H22 N3 C4 MG O H1 H2 O H1 H2 O H1 H2 ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
