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-- John D. Chodera QB3-Berkeley Fellow, University of California, Berkeley email: jchodera.gmail.com mobile: 415.867.7384 url: http://www.choderalab.org ---------- Forwarded message ---------- From: John Chodera <jchodera.gmail.com> Date: 2008/10/26 Subject: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 To: amber.scripps.edu Hi all, I just noticed that the copy of gaff.dat (the GAFF parameter definition file) appearing in AmberTools 1.2 contains repeated entries, but with these entries specifying different parameters. For example, in the bond section: cd-cd 418.3 1.429 SOURCE1 740 0.0058 0.0069 cd-cd 504.0 1.371 SOURCE3 523 same as cc-cd A complete list of duplicate lines is attached below. This occurs both in amber10/dat/leap/parm/gaff.dat and amber10/dat/leap/gleap/gaff.dat. Can anyone comment on which entry (the first or second) is correct, and which entry LEaP would have been using (first or second)? This issue appears to have been dealt with via a bugfix in the AMBER8 release: http://ambermd.org/bugfixes/8.0/bugfix.28 but the buggy file (if this is indeed unintended) appears to have crept back into the release versions somewhere along the line. Applying this patch appears to fix the problems, but some patches are rejected (also attached below). This was also mentioned on the mail reflector as recently as June of this year: http://archive.ambermd.org/200806/0289.html but it appears to remain unrectified in the AmberTools 1.2 distribution put out in July. Thanks go out to D. E. Shaw Research guys on this: I've been working on AmberTools GAFF -> Desmond conversion scripts, and their forcefield conversion tools detected and enumerated the duplicate entries in gaff.dat. Thanks! John -- John D. Chodera QB3-Berkeley Fellow, University of California, Berkeley url: http://www.choderalab.org mobile: 415.867.7384 email: jchodera.berkeley.edu -- Complete list of duplicated entries: lines 336-337 cd-cd 418.3 1.429 SOURCE1 740 0.0058 0.0069 cd-cd 504.0 1.371 SOURCE3 523 same as cc-cd lines 371-372 cf-cf 390.5 1.451 SOURCE1 66 0.0060 0.0060 cf-cf 562.4 1.338 SOURCE1 543 same as ce-cf lines 392-393 ch-ch 494.2 1.377 SOURCE1 42 0.0000 0.0000 ch-ch 949.5 1.191 SOURCE1 80 same as cg-ch lines 541-542 n1-n1 1221.7 1.124 SOURCE1 19 0.0000 0.0000 n1-n1 1365.7 1.100 SOURCE3 lines 653-654 nd-nd 486.8 1.379 SOURCE3 9 0.0145 0.0164 nd-nd 602.9 1.315 SOURCE3 9 same as nc-nd lines 668-669 nf-nf 355.3 1.479 SOURCE3 19 same as ne-ne nf-nf 738.6 1.257 SOURCE3 1 same as ne-nf lines 789-790 pf-pf 240.7 2.092 SOURCE3 7 same as pe-pe pf-pf 260.8 2.055 SOURCE3 1 same as pe-pf lines 2076 and 4277 n1-n1-s 54.6 180.00 SOURCE3 1 0.0000 0.0000 n1-n1-s 54.6 179.96 HF/6-31G* lines 1042 and 4285 n1-c1-n1 93.2 102.01 SOURCE0 1 n1-c1-n1 70.2 180.00 HF/6-31G* Rejected patches from bugfix.28 for AMBER8 applied to gaff.dat in AmberTools-1.2 *************** *** 4224,4230 **** c1-n1-o 62.6 179.95 HF/6-31G* c1-n1-oh 62.9 174.31 HF/6-31G* c1-n1-os 62.2 176.61 HF/6-31G* ! c1-n1-p1 83.5 172.83 HF/6-31G* c1-n1-p3 68.7 173.51 HF/6-31G* c1-n1-p4 68.7 173.64 HF/6-31G* c1-n1-p5 71.5 177.28 HF/6-31G* --- 4216,4222 ---- c1-n1-o 62.6 179.95 HF/6-31G* c1-n1-oh 62.9 174.31 HF/6-31G* c1-n1-os 62.2 176.61 HF/6-31G* ! c1-n1-p2 83.5 172.83 HF/6-31G* c1-n1-p3 68.7 173.51 HF/6-31G* c1-n1-p4 68.7 173.64 HF/6-31G* c1-n1-p5 71.5 177.28 HF/6-31G* *************** *** 5061,5075 **** hc-o -c -oh 1.1 180. 2. Junmei et al.1999 hc-o -c -os 1.1 180. 2. n2-c2-ca-n2 1.1 180. 2. dac guess, 9/94 - n2-ca-ca-c3 1.1 180. 2. n2-ca-ca-n2 1.1 180. 2. dac guess, 9/94 - na-ca-ca-c3 1.1 180. 2. na-n2-ca-n2 1.1 180. 2. dac, 10/94 X -X -X -X 1.1 180. 2. dac, 10/94 hw ow 0000. 0000. 4. flag for fast water - n na n2 MOD4 RE h1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963 --- 5046,5057 ---- hc-o -c -oh 1.1 180. 2. Junmei et al.1999 hc-o -c -os 1.1 180. 2. n2-c2-ca-n2 1.1 180. 2. dac guess, 9/94 n2-ca-ca-n2 1.1 180. 2. dac guess, 9/94 na-n2-ca-n2 1.1 180. 2. dac, 10/94 X -X -X -X 1.1 180. 2. dac, 10/94 hw ow 0000. 0000. 4. flag for fast water MOD4 RE h1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963 ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo.scripps.eduReceived on Fri Dec 05 2008 - 15:55:36 PST