AMBER Archive (2006)

Subject: AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand

From: Christophe Guilbert (cguilbert_at_picasso.ucsf.edu)
Date: Fri Jun 16 2006 - 23:32:12 CDT

Hi everyone,

I am using Antechamber 1.25 and Amber 8 (tleap ) to calculate the
charges , topology and parameter of a ligand (see attachment in mol2)
When I use CHARMM (using charmmgen) or my own program to minimized this
ligand, I have C7 , N3, N1 and N2 becoming not planar after
minimization. this structure contains 10 improper Angle (according to
antechamber) , everything should be planar , I can only obtain a flat
ligand when increasing the improper angle force constant from 1.1
Kcal/mole to 10Kcal/mol. I don't see what's wrong with the topology and
parameter. I would greatly appreciate any thought about it.

Could anyone try my ligand and minimize it with Amber to check if they
have the same result ?

Here is my script

antechamber -nc 1 -rn lig -i tobeconvert.mol2 -fi mol2 -o lig_bcc.mol2
-fo mol2 -c bcc -j 4 -at gaff
parmchk -i lig_bcc.mol2 -f mol2 -o lig_bcc.frcmod

here is the leap.inp file:
--------------------------------------------------
source leaprc.gaff
mods = LoadAmberParams lig_bcc.frcmod
lig = loadMol2 lig_bcc.mol2
saveAmberParm lig lig_bcc.prmtop lig_bcc.prmcrd
quit
---------------------------------------------------

tleap -f leap.inp

Thanks

Chris 

-- 
--------------------------------------------------------------------------
Christophe Guilbert, Ph.D.
Mission Bay Genentech Hall
UCSF, Department of Pharmaceutical Chemistry
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Office      : 415-476-0707
Office fax  : 415-476-0688
Email: cguilbert_at_picasso.ucsf.edu
http://mondale.ucsf.edu
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@<TRIPOS>MOLECULE
ZINC00157587
   18 19 0 0 0
SMALL
USER_CHARGES
1H-benzoimidazol-2-amine
@<TRIPOS>ATOM
      1 C1 2.4380 2.5514 2.5630 C.ar 1 <0> -0.1500
      2 C2 1.5891 2.8096 3.6607 C.ar 1 <0> -0.1500
      3 C3 2.0882 2.9626 4.9624 C.ar 1 <0> -0.1090
      4 C4 3.4663 2.8433 5.0949 C.ar 1 <0> 0.3090
      5 C5 4.3062 2.5879 4.0089 C.ar 1 <0> 0.3090
      6 C6 3.8275 2.4338 2.7136 C.ar 1 <0> -0.1090
      7 N1 5.5867 2.5379 4.5203 N.pl3 1 <0> -0.8667
      8 C7 5.5588 2.7470 5.8381 C.cat 1 <0> 1.0700
      9 N2 6.6306 2.7671 6.6623 N.pl3 1 <0> -0.8367
     10 H1 6.4257 2.3671 3.9744 H 1 <0> 0.4500
     11 H2 6.5187 2.9344 7.6577 H 1 <0> 0.4500
     12 H3 7.5677 2.6154 6.3013 H 1 <0> 0.4500
     13 H4 2.0009 2.4408 1.5726 H 1 <0> 0.1500
     14 H5 0.5173 2.8919 3.4909 H 1 <0> 0.1500
     15 H6 1.4486 3.1608 5.8127 H 1 <0> 0.1500
     16 H7 4.4896 2.2361 1.8806 H 1 <0> 0.1500
     17 N3 4.2877 2.9328 6.1999 N.pl3 1 <0> -0.8667
     18 H8 3.9715 3.1134 7.1477 H 1 <0> 0.4500
@<TRIPOS>BOND
     1 1 6 ar
     2 1 2 ar
     3 1 13 1
     4 2 3 ar
     5 2 14 1
     6 3 4 ar
     7 3 15 1
     8 4 5 ar
     9 4 17 1
    10 5 6 ar
    11 5 7 1
    12 6 16 1
    13 7 8 1
    14 7 10 1
    15 8 9 1
    16 8 17 2
    17 9 11 1
    18 9 12 1
    19 17 18 1

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