AMBER Archive (2006)

Subject: RE: AMBER: Parmchk problems (parm99.dat)

From: Prashanth Athri (athriprashanth_at_yahoo.com)
Date: Tue Sep 12 2006 - 12:10:55 CDT

 Thanks for the reply-- here are the files. I am using the standard parm99.dat distribution of AMBER8

ante_output.mol2
-----------------------------------------------------------------------------------------------------------------------
@<TRIPOS>MOLECULE
Default_Mol
   25 27 1 0 0
SMALL
No Charge or Current Charge
 
 
@<TRIPOS>ATOM
      1 N1 0.9000 -0.7640 0.0000 NB 1 N2 -0.4347
      2 C2 0.2200 -1.8350 0.0000 CB 1 N2 0.5714
      3 C3 0.6740 -3.2190 0.0000 CA 1 N2 -0.2615
      4 H4 1.7260 -3.4290 0.0000 HA 1 N2 0.2347
      5 C5 -0.2720 -4.1610 0.0000 CA 1 N2 -0.0241
      6 H6 -0.0210 -5.2050 0.0000 HA 1 N2 0.1869
      7 C7 -1.6930 -3.8090 0.0000 CA 1 N2 0.0866
      8 H8 -2.3950 -4.6240 0.0000 HA 1 N2 0.2252
      9 C9 -2.1930 -2.5210 0.0000 CA 1 N2 -0.2458
     10 H10 -3.2480 -2.3240 0.0000 HA 1 N2 0.2146
     11 C11 -1.2370 -1.5300 0.0000 CB 1 N2 0.2539
     12 N12 -1.2940 -0.1980 0.0000 N* 1 N2 -0.3287
     13 H13 -2.1350 0.3420 0.0000 H 1 N2 0.3765
     14 C14 0.0000 0.3010 0.0000 CK 1 N2 0.3746
     15 C15 0.3950 1.6080 0.0000 CA 1 N2 0.0697
     16 C16 1.8110 1.8940 0.0000 CA 1 N2 0.0458
     17 H17 2.5060 1.0770 0.0000 HA 1 N2 0.1440
     18 C18 2.2470 3.1840 0.0000 CA 1 N2 -0.1007
     19 H19 3.2960 3.4100 0.0000 HA 1 N2 0.1728
     20 C20 1.3070 4.2220 0.0000 CA 1 N2 0.0700
     21 H21 1.6530 5.2400 0.0000 HA 1 N2 0.2062
     22 C22 -0.0910 3.9800 0.0000 CA 1 N2 -0.0356
     23 H23 -0.7720 4.8090 0.0000 HA 1 N2 0.1705
     24 C24 -0.5430 2.7060 0.0000 CA 1 N2 -0.1582
     25 H25 -1.6010 2.5230 0.0000 HA 1 N2 0.1859
@<TRIPOS>BOND
     1 1 2 1
     2 1 14 2
     3 2 3 ar
     4 2 11 ar
     5 3 4 1
     6 3 5 ar
     7 5 6 1
     8 5 7 ar
     9 7 8 1
    10 7 9 ar
    11 9 10 1
    12 9 11 ar
    13 11 12 1
    14 12 13 1
    15 12 14 1
    16 14 15 1
    17 15 16 ar
    18 15 24 ar
    19 16 17 1
    20 16 18 ar
    21 18 19 1
    22 18 20 ar
    23 20 21 1
    24 20 22 ar
    25 22 23 1
    26 22 24 ar
    27 24 25 1
@<TRIPOS>SUBSTRUCTURE
     1 N2 1 TEMP 0 **** **** 0 ROOT
------------------------------------------------------------------------------------------------------------------
parmchk_output for the following command:
"parmchk -p $AMBERHOME/dat/leap/parm/parm99.dat -i antechamber_output.mol2 -f mol2 -o missing parm.frcmod"
-------------------------------------------------------------------------------------------------------------------
remark goes here
MASS
 
BOND
CA-HA 0.00 0.000 ATTN, need revision
N*-H 0.00 0.000 ATTN, need revision
CK-CA 0.00 0.000 ATTN, need revision
 
ANGLE
NB-CB-CA 0.000 0.000 ATTN, need revision
NB-CB-CB 0.000 0.000 ATTN, need revision
NB-CK-N* 0.000 0.000 ATTN, need revision
NB-CK-CA 0.000 0.000 ATTN, need revision
CB-NB-CK 0.000 0.000 ATTN, need revision
CB-CA-HA 0.000 0.000 ATTN, need revision
CB-CA-CA 0.000 0.000 ATTN, need revision
CB-CB-CA 0.000 0.000 ATTN, need revision
CB-CB-N* 0.000 0.000 ATTN, need revision
CA-CA-HA 0.000 0.000 ATTN, need revision
CA-CA-CA 0.000 0.000 ATTN, need revision
CA-CB-N* 0.000 0.000 ATTN, need revision
CB-N*-H 0.000 0.000 ATTN, need revision
CB-N*-CK 0.000 0.000 ATTN, need revision
N*-CK-CA 0.000 0.000 ATTN, need revision
H -N*-CK 0.000 0.000 ATTN, need revision
CK-CA-CA 0.000 0.000 ATTN, need revision
 
DIHE
NB-CB-CA-HA 1 0.000 0.000 0.000 ATTN, need revision
NB-CB-CA-CA 1 0.000 0.000 0.000 ATTN, need revision
NB-CB-CB-CA 1 0.000 0.000 0.000 ATTN, need revision
NB-CB-CB-N* 1 0.000 0.000 0.000 ATTN, need revision
NB-CK-N*-CB 1 0.000 0.000 0.000 ATTN, need revision
NB-CK-N*-H 1 0.000 0.000 0.000 ATTN, need revision
NB-CK-CA-CA 1 0.000 0.000 0.000 ATTN, need revision
CB-NB-CK-N* 1 0.000 0.000 0.000 ATTN, need revision
CB-NB-CK-CA 1 0.000 0.000 0.000 ATTN, need revision
CB-CA-CA-HA 1 0.000 0.000 0.000 ATTN, need revision
CB-CA-CA-CA 1 0.000 0.000 0.000 ATTN, need revision
CB-CB-CA-CA 1 0.000 0.000 0.000 ATTN, need revision
CB-CB-CA-HA 1 0.000 0.000 0.000 ATTN, need revision
CB-CB-N*-H 1 0.000 0.000 0.000 ATTN, need revision
CB-CB-N*-CK 1 0.000 0.000 0.000 ATTN, need revision
CA-CB-NB-CK 1 0.000 0.000 0.000 ATTN, need revision
CA-CB-CB-CA 1 0.000 0.000 0.000 ATTN, need revision
CA-CB-CB-N* 1 0.000 0.000 0.000 ATTN, need revision
CA-CA-CA-HA 1 0.000 0.000 0.000 ATTN, need revision
CA-CA-CA-CA 1 0.000 0.000 0.000 ATTN, need revision
HA-CA-CA-HA 1 0.000 0.000 0.000 ATTN, need revision
CA-CA-CB-N* 1 0.000 0.000 0.000 ATTN, need revision
CA-CB-N*-H 1 0.000 0.000 0.000 ATTN, need revision
CA-CB-N*-CK 1 0.000 0.000 0.000 ATTN, need revision
HA-CA-CB-N* 1 0.000 0.000 0.000 ATTN, need revision
CB-CB-NB-CK 1 0.000 0.000 0.000 ATTN, need revision
CB-N*-CK-CA 1 0.000 0.000 0.000 ATTN, need revision
N*-CK-CA-CA 1 0.000 0.000 0.000 ATTN, need revision
H -N*-CK-CA 1 0.000 0.000 0.000 ATTN, need revision
CK-CA-CA-HA 1 0.000 0.000 0.000 ATTN, need revision
CK-CA-CA-CA 1 0.000 0.000 0.000 ATTN, need revision
 
IMPROPER
CB-NB-CA-CB 1.1 180.0 2.0 Using default value
CA-CB-HA-CA 1.1 180.0 2.0 Using default value
CA-CA-HA-CA 1.1 180.0 2.0 Using default value
CA-CA-HA-CB 1.1 180.0 2.0 Using default value
CB-CB-CA-N* 1.1 180.0 2.0 Using default value
N*-CB-H -CK 1.1 180.0 2.0 Using default value
CK-NB-N*-CA 1.1 180.0 2.0 Using default value
CA-CK-CA-CA 1.1 180.0 2.0 Using default value
CA-CA-CA-HA 1.1 180.0 2.0 Using default value
 
NONBON
  NB 0.0000 0.0000 ATTN, need revision
  CB 0.0000 0.0000 ATTN, need revision
  CA 0.0000 0.0000 ATTN, need revision
  N* 0.0000 0.0000 ATTN, need revision
  CK 0.0000 0.0000 ATTN, need revision
-------------------------------------------------------------------------------------------------------------------------

Prashanth Athri <athriprashanth_at_yahoo.com> wrote: Thanks for the reply-- here are the files.
I have attached a copy of the parm99.dat file that I use as well.

In the .frcmod file, theree are a lot of parameters that are already parameterized in the parm99.dat file. (using Amber 8)

Junmei Wang <jwang_at_encysive.com> wrote:Message Please attach the trouble molecules. I tested parmchk with phenol by using similar commands you used and it works fine.
  
 All the best
  
 Junmei
  
 
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Prashanth Athri
Sent: Sunday, September 10, 2006 7:23 PM
To: amber_at_scripps.edu
Subject: AMBER: Parmchk problems (parm99.dat)

 Dear users:

[I have tried to use the most updated antechamber as suggested by previous threads....this gives the same problem.]

When I run use
"antechamber -at amber ......"
the output has amber atomtypes (as expected)

Now, when I run
"parmchk -p $AMBERHOME/dat/leap/parm/parm99.dat -i antechamber_output.mol2 -f mol2 -o missing parm.frcmod"

The output does not reflect the parameters that are present in parm99.dat. Instead most parameters are shown to be missing(all values are zerous, i.e the ff params). Is there anything obviously wrong in what I am doing?

I am trying to some dihedral calculations on benzimidazole- phenyl system. This problem is with respect to the benzimidazole, which has a five membered ring very similar to the Ade, Gua systems, hence the use of parm99.dat

Ofcourse I can manually change every value, does anyone have other suggestions? Thx in advance.
-Prashanth

    

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