AMBER Archive (2009)

Subject: [AMBER] atom type

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Thu Jun 04 2009 - 20:03:14 CDT

Hi,

I have a molecule that i would like to use in my simulation, i can get
the missing parameters from Antechamber, but i prefer to get the charges
from antechamber but use the forcefield already defined in gaff.dat.
However, in xleap i get missing parameters
Checking parameters for unit 'smcc'.
Checking for bond parameters.
Checking for angle parameters.
Could not find angle parameter: c3 - n3 - c2
Could not find angle parameter: c3 - n3 - c2
Could not find angle parameter: n3 - c2 - c3
Could not find angle parameter: n3 - c2 - o
Could not find angle parameter: n3 - c2 - c3
Could not find angle parameter: n3 - c2 - o
There are missing parameters.
check: Warnings: 4
Unit is OK.

i looked at the 'Development and Testing of a General Amber Force Field'
article and i am still not sure why would gaff not have the above
parameters unless there is something wrong with my atom types or my
structure. What is the atom type of a nitrogen connected to three
carbons? as far as i can tell it should be n3.

also, since i sent the mol2 file, the bond between c2 and o is a double
bond, shouldn't there be a number 2 in the fourth column under
@<TRIPOS>BOND? unless the number in the fourth column is inconsequential
since the bond force and length in the forcefield file is what matters.

Thank you for your help,
Taufik


@<TRIPOS>MOLECULE
SMCC
   50 51 1 0 1
SMALL
USER_CHARGES
@<TRIPOS>ATOM
  1 C1 0.000000 0.000000 0.000000 c2 1 SMC 0.6640 ****
  2 C2 1.505000 0.000000 0.000000 c3 1 SMC -0.1224 ****
  3 O3 -0.670000 1.032000 0.000000 o 1 SMC -0.6157 ****
  4 C5 2.036000 0.911000 -1.102000 c3 1 SMC -0.0680 ****
  5 C6 2.064000 -1.406000 -0.152000 c3 1 SMC -0.0727 ****
  6 C7 3.499000 0.775000 -1.232000 c3 1 SMC -0.0798 ****
  7 C8 4.208000 -0.513000 -1.111000 c3 1 SMC -0.0796 ****
  8 C9 3.574000 -1.397000 -0.044000 c3 1 SMC -0.0817 ****
  9 C10 5.644292 -0.257497 -0.631894 c3 1 SMC 0.0901 ****
 10 N11 6.253000 0.798000 -1.493000 n3 1 SMC -0.5038 ****
 11 C12 5.437000 1.921000 -1.714000 c2 1 SMC 0.7010 ****
 12 C13 7.604000 1.193000 -1.540000 c2 1 SMC 0.7040 ****
 13 C14 6.214000 3.142000 -2.094000 c3 1 SMC -0.1469 ****
 14 C15 7.677000 2.663000 -1.984000 c3 1 SMC -0.0959 ****
 15 O16 4.121000 1.918000 -1.581000 o 1 SMC -0.5790 ****
 16 O17 8.560000 0.457000 -1.274000 o 1 SMC -0.5993 ****
 17 S19 8.421000 2.900000 -3.563000 ss 1 SMC -0.2559 ****
 18 C20 10.121000 2.503000 -3.266000 c3 1 SMC -0.0250 ****
 19 C21 10.801000 2.433000 -4.609000 c3 1 SMC -0.0724 ****
 20 C22 12.284000 2.163000 -4.449000 c3 1 SMC -0.0792 ****
 21 C23 12.971000 2.080000 -5.796000 c3 1 SMC -0.0798 ****
 22 C24 14.453000 1.814000 -5.641000 c3 1 SMC -0.1023 ****
 23 C25 15.141000 1.729000 -6.979000 c3 1 SMC 0.1690 ****
 24 H48 12.818000 3.039000 -6.357000 hc 1 SMC 0.0404 ****
 25 H49 12.504000 1.262000 -6.406000 hc 1 SMC 0.0400 ****
 26 H50 14.603000 0.855000 -5.078000 hc 1 SMC 0.0358 ****
 27 H51 14.918000 2.631000 -5.029000 hc 1 SMC 0.0365 ****
 28 H54 15.024000 2.685000 -7.544000 hc 1 SMC 0.0307 ****
 29 H57 1.837000 0.414000 0.996000 hc 1 SMC 0.0558 ****
 30 H58 1.746000 1.973000 -0.881000 hc 1 SMC 0.0450 ****
 31 H59 1.553000 0.629000 -2.079000 hc 1 SMC 0.0436 ****
 32 H60 1.756000 -1.825000 -1.146000 hc 1 SMC 0.0464 ****
 33 H61 1.639000 -2.070000 0.645000 hc 1 SMC 0.0416 ****
 34 H64 4.128000 -1.042000 -2.108000 hc 1 SMC 0.0519 ****
 35 H65 3.965000 -2.442000 -0.157000 hc 1 SMC 0.0446 ****
 36 H66 3.872000 -1.033000 0.976000 hc 1 SMC 0.0449 ****
 37 H67 6.178330 -1.101376 -0.667057 h1 1 SMC 0.0421 ****
 38 H68 5.616853 0.083371 0.308271 h1 1 SMC 0.0455 ****
 39 H69 6.010000 3.984000 -1.388000 hc 1 SMC 0.0736 ****
 40 H70 5.956000 3.473000 -3.134000 hc 1 SMC 0.0707 ****
 41 H71 8.237000 3.226000 -1.196000 h1 1 SMC 0.1001 ****
 42 H72 10.200000 1.527000 -2.724000 h1 1 SMC 0.0603 ****
 43 H73 10.593000 3.288000 -2.627000 h1 1 SMC 0.0608 ****
 44 H74 10.654000 3.398000 -5.163000 hc 1 SMC 0.0500 ****
 45 H75 10.338000 1.618000 -5.228000 hc 1 SMC 0.0501 ****
 46 H76 12.433000 1.202000 -3.890000 hc 1 SMC 0.0414 ****
 47 H77 12.753000 2.978000 -3.837000 hc 1 SMC 0.0405 ****
 48 H78 14.708000 0.903000 -7.593000 hc 1 SMC 0.0303 ****
 49 H51 3.655564 1.739183 -1.291624 hc 1 SMC 0.0609 ****
 50 H52 4.031520 0.952147 -2.055437 hc 1 SMC 0.0478 ****
@<TRIPOS>BOND
    1 1 2 1
    2 1 3 1
    3 2 4 1
    4 2 5 1
    5 2 29 1
    6 4 6 1
    7 4 30 1
    8 4 31 1
    9 5 8 1
   10 5 32 1
   11 5 33 1
   12 6 7 1
   13 6 49 1
   14 6 50 1
   15 7 8 1
   16 7 9 1
   17 7 34 1
   18 8 35 1
   19 8 36 1
   20 9 10 1
   21 9 37 1
   22 9 38 1
   23 10 11 1
   24 10 12 1
   25 11 13 1
   26 11 15 1
   27 12 14 1
   28 12 16 1
   29 13 14 1
   30 13 39 1
   31 13 40 1
   32 14 17 1
   33 14 41 1
   34 17 18 1
   35 18 19 1
   36 18 42 1
   37 18 43 1
   38 19 20 1
   39 19 44 1
   40 19 45 1
   41 20 21 1
   42 20 46 1
   43 20 47 1
   44 21 22 1
   45 21 24 1
   46 21 25 1
   47 22 23 1
   48 22 26 1
   49 22 27 1
   50 23 28 1
   51 23 48 1
@<TRIPOS>SUBSTRUCTURE
      1 SMC 1 **** 0 **** ****


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