amber-developers: FW: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 from Ross Walker on 2008-10-30 (Amber Archive Oct 2008)

From: Ross Walker <ross.rosswalker.co.uk>
Date: Thu, 30 Oct 2008 10:41:27 -0700

Since nobody seemed to want to answer this and it seems quite serious I am
posting this to the Amber Developers list so that it doesn't get lost.

-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
John Chodera
Sent: Sunday, October 26, 2008 6:17 PM
To: amber.scripps.edu
Subject: AMBER: Duplicate entries with different parameters in gaff.dat from
AmberTools 1.2

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
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Received on Fri Oct 31 2008 - 05:11:15 PDT