AMBER Archive (2004)

Subject: AMBER: how to correctly change frcmod?

From: opitz_at_che.udel.edu
Date: Fri Jan 23 2004 - 17:05:38 CST

('binary' encoding is not supported, stored as-is) Dear Amber Community,

I am just beginning to use Amber 7. I am trying to simulate a dendrimer
whose pdb file I already have. This pdb file contains all atoms, except
the hydrogens, as those gave me problems. After removing the hydrogens
from my pdb file, antechamber accepted the file and gave me the prepin
file (antechamber –i file.pdb –fi pdb –o file.prepin –fo prepi) (found
below). Once I had the prepin file I ran parmchk (parmchk –i file.prepin
–f prepi –o frcmod). In the frcmod several parameters were missing, so I
found those and put them in the file.
When trying to read the frcmod file into leap I get the error message:

> source leaprc.gaff
----- Source: /usr/local/amber7/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber7/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber7/dat/leap/parm/gaff.dat
> mods = loadamberparams frcmod
Loading parameters: ./frcmod
Reading force field mod type file (frcmod)
Unknown keyword:
 in parameter file.
Unknown keyword:
 in parameter file.

Does anybody know what causes this?

Here I will attach in this order the first 2 pages of the prepin file and
the frcmod file.

remark goes here
MASS
DU 14.01 0.530 ATTN, need revision

BOND
DU-c1 515.1 1.320 ATTN, need revision

ANGLE
DU-c1-c1 62.000 180.000 ATTN, need revision
c1-n2-c 63.956 122.450 Calculated with empirical approach
n2-c -c1 68.143 112.815 Calculated with empirical approach

DIHE

IMPROPER
c1-DU-c1-o 1.1 180.0 2.0 Using default value

NONBON
  DU 1.8240 0.1700 ATTN, need revision

    0 0 2

This is a remark line
molecule.res
NH2 XYZ 0
CORRECT OMIT DU BEG
  0.0000
   1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
   2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
   3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
   4 N DU M 3 2 1 1.540 111.208 180.000 0.000
   5 C2 c1 M 4 3 2 1.438 115.985 117.358 0.000
   6 C1 c1 M 5 4 3 1.510 103.619 -8.175 0.000
   7 N n2 M 6 5 4 1.418 112.521 -179.444 0.000
   8 C1 c M 7 6 5 1.369 126.496 -126.546 0.000
   9 O2 o E 8 7 6 1.262 123.106 -2.288 0.000
  10 C2 c1 M 8 7 6 1.544 115.521 -179.608 0.000
  11 C1 c1 M 10 8 7 1.501 110.416 -161.819 0.000
  12 N1 n3 M 11 10 8 1.448 118.657 179.384 0.000
  13 C2 c1 S 12 11 10 1.497 119.791 -57.213 0.000
  14 C1 c1 S 13 12 11 1.510 112.725 -46.800 0.000
  15 C1 c B 14 13 12 1.566 116.398 -64.684 0.000
  16 O2 o E 15 14 13 1.197 120.317 -65.770 0.000
  17 N n2 S 15 14 13 1.355 117.544 118.319 0.000
  18 C1 c1 S 17 15 14 1.534 125.845 -175.947 0.000
  19 C2 c1 S 18 17 15 1.549 112.099 59.043 0.000
  20 N DU E 19 18 17 1.441 109.088 80.380 0.000
  21 C1 c1 M 12 11 10 1.486 116.160 162.895 0.000
  22 C2 c1 M 21 12 11 1.588 110.667 -51.521 0.000
  23 N1 n2 M 22 21 12 1.536 107.329 -166.287 0.000
  24 C1 c M 23 22 21 1.317 126.665 135.019 0.000
  25 O2 o E 24 23 22 1.227 116.178 -175.342 0.000
  26 C1 c1 M 24 23 22 1.473 122.913 0.331 0.000
  27 C2 c1 M 26 24 23 1.603 110.646 68.963 0.000
  28 N1 n3 M 27 26 24 1.478 111.178 -164.361 0.000
  29 C2 c1 S 28 27 26 1.469 120.437 -84.994 0.000
  30 C1 c1 S 29 28 27 1.579 111.399 -141.638 0.000
  31 C1 c B 30 29 28 1.546 113.303 168.891 0.000
  32 O2 o E 31 30 29 1.230 118.711 26.022 0.000
  33 N1 n2 S 31 30 29 1.340 122.121 -160.074 0.000
  34 C2 c1 S 33 31 30 1.492 120.570 -5.556 0.000
  35 C1 c1 S 34 33 31 1.555 108.185 -166.004 0.000
  36 N1 n3 B 35 34 33 1.505 113.663 92.759 0.000
  37 C1 c1 S 36 35 34 1.470 115.189 88.529 0.000
  38 C2 c1 S 37 36 35 1.557 109.463 -98.566 0.000
  39 C1 c B 38 37 36 1.530 110.294 168.300 0.000
  40 N n2 S 39 38 37 1.298 118.880 124.726 0.000
  41 C1 c1 S 40 39 38 1.390 123.636 176.330 0.000
  42 C2 c1 S 41 40 39 1.582 114.427 99.547 0.000
  43 N DU E 42 41 40 1.419 104.056 162.775 0.000
  44 O2 o E 39 38 37 1.222 121.794 -54.794 0.000
  45 C2 c1 S 36 35 34 1.463 115.739 -58.611 0.000
  46 C1 c1 S 45 36 35 1.541 118.693 -158.894 0.000
  47 C1 c B 46 45 36 1.532 112.151 74.276 0.000
  48 O2 o E 47 46 45 1.232 117.372 10.627 0.000
  49 N n2 S 47 46 45 1.372 118.400 -176.297 0.000
  50 C1 c1 S 49 47 46 1.441 130.898 8.194 0.000
  51 C2 c1 S 50 49 47 1.565 114.502 166.734 0.000
  52 N DU E 51 50 49 1.448 104.329 -85.136 0.000

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