AMBER Archive (2007)

Subject: Re: AMBER: antechamber fails with large molecules

From: Junmei Wang (junmwang_at_yahoo.com)
Date: Fri Nov 02 2007 - 00:16:41 CST


Personally I don't think there is a good approach to get good charges (such as HF/6-31G* RESP). AM1BCC may be a good candidate. The problem is that antechamber may not handle such large molecules well. In amber10, I have improved the code a little bit to handle large molecules much better, in a long run I also plan to develop a even simpler, but more reliable charges (compared to am1-bcc) for arbitrary organic molecules. This method will be available in amber11. Best Junmei ----- Original Message ---- From: Francesco Pietra <chiendarret_at_yahoo.com> To: amber_at_scripps.edu Sent: Thursday, November 1, 2007 3:29:26 AM Subject: Re: AMBER: antechamber fails with large molecules You may remeber that I tried unsuccessfully to get the partial charges with Antechamber in Amber9 for a 500-atoms non-repetitive molecule. Prof Case, and others, suggested, however, that, even if calculated, the partial charges would be unreliable for such a large residue. Is the new code intended to solve this question too? At any event, do you plan to make the new code available? An when? I have frequently problems of large ligands. Thanks francesco pietra --- Junmei Wang <junmwang_at_yahoo.com> wrote: > Could you send me the file? I have modified the respgen.c code a little bit > to handle large molecules, but it is not in amber9. > > Best > > Junmei > > Dear amber users: > > I am trying fit RESP charges with antechamber to a large > organic molecule (342 atoms) with the command: > > antechamber –i biscalix.log –fi gout –o biscalix_resp.mol2 > -fo mol2 –c resp > > This fitting process failed with the following errors: > > “The number of the path atoms exceeds > MAXPATHATOMNUM(1900000) for atom[148],extend the size and > reallocate the memory automatically reallocate memory for > pathscore[148] failed > Info: the atom number exceeds the MAXATOM, reallocate > memory automatically > Amber 9 RESP > Unit 5 Error on OPEN: ANTECHAMBER_RESP1.IN > Error: cannot run "resp -O -i ANTECHAMBER_RESP1.IN -o > ANTECHAMBER_RESP1.OUT -e ANTECHAMBER.ESP -t qout" in > resp() of charge.c properly, exit”. > > Could someone give me any idea about how to solve this > type of problems? > > Thanks in advance, > Vânia Calisto > > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
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