*Dear amber users.*
*I studied ANTECHAMBER tutorial
(
http://ambermd.org/tutorials/basic/tutorial4b/
<
http://ambermd.org/tutorials/basic/tutorial4b/>) accurately.*
*My system is a complex containing protein + ligand (sal1)*
*complex = comp1.pdb*
*ligand = sal1.pdb containing 10 atoms.*
*According to the ANTECHAMBER tutorial, I used following commands:*
$AMBERHOME/exe/reduce sal1.pdb > sal1_h.pdb ****** **6 H atoms were
added.*
$AMBERHOME/exe/antechamber -i sal1_h.pdb -fi pdb -o sal1_h.mol2 -fo mol2 -c
bcc -s 2
$AMBERHOME/exe/parmchk -i sal1_h.mol2 -f mol2 -o sal1_h.frcmod
$AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03
source leaprc.gaff
sal1_h = loadmol2 sal1_h.mol2
check sal1_h
*******
*Checking 'sal1_h'....*
*Checking parameters for unit 'sal1_h'.*
*Checking for bond parameters.*
*Checking for angle parameters.*
*Unit is OK.*
loadamberparams sal1_h.frcmod
saveoff sal1_h.lib
saveamberparams sal1_h sal1_h.prmtop sal1_h.inpcrd
quit
sal1
****** sal1_h.prmtop sal1_h.inpcrd file were created without problem.*
*sal1_h.frcmod, sal1_h.mol2, sal1_h.lib, sal1_h. inpcrd and sal1_h.prmtop
files are as follows:*
==========================================================================
*sal1_h.frcmod file:*
remark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
ca-o -c -oh 10.5 180.0 2.0 General
improper torsional angle (2 general atom types)
c -ca-ca-ca 1.1 180.0 2.0 Using default
value
ca-ca-ca-oh 1.1 180.0 2.0 Using default
value
ca-ca-ca-ha 1.1 180.0 2.0 General
improper torsional angle (2 general atom types)
NONBON
==========================================================================
*sal1_h.mol2 file:*
.<TRIPOS>MOLECULE
SAL
16 16 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 C1' 31.0710 2.7490 30.8340 c 1100 SAL 0.664700
2 O1' 30.3390 2.1300 31.7220 o 1100 SAL -0.589000
3 O2' 31.4840 3.9370 31.1730 oh 1100 SAL -0.597100
4 C1 31.4300 2.1690 29.5250 ca 1100 SAL -0.234600
5 C2 31.0010 0.8230 29.0650 ca 1100 SAL 0.208100
6 C3 31.3910 0.2640 27.7240 ca 1100 SAL -0.184000
7 C4 32.2210 1.0830 26.8490 ca 1100 SAL -0.057000
8 C5 32.6770 2.4280 27.2450 ca 1100 SAL -0.188000
9 C6 32.2690 2.9450 28.5820 ca 1100 SAL -0.033000
10 O2 30.1900 -0.0260 29.8630 oh 1100 SAL -0.498100
11 HO2' 31.5940 3.9810 32.1660 ho 1100 SAL 0.451000
12 HO2 29.9880 0.4260 30.7320 ho 1100 SAL 0.461000
13 H6 32.6060 3.9480 28.8820 ha 1100 SAL 0.156000
14 H5 33.3020 3.0340 26.5720 ha 1100 SAL 0.142000
15 H4 32.5150 0.6860 25.8660 ha 1100 SAL 0.140000
16 H3 31.0580 -0.7370 27.4120 ha 1100 SAL 0.158000
.<TRIPOS>BOND
1 1 2 2
2 1 3 1
3 1 4 1
4 3 11 1
5 4 5 ar
6 4 9 ar
7 5 6 ar
8 5 10 1
9 6 7 ar
10 6 16 1
11 7 8 ar
12 7 15 1
13 8 9 ar
14 8 14 1
15 9 13 1
16 10 12 1
.<TRIPOS>SUBSTRUCTURE
1 SAL 1 TEMP 0 **** **** 0 ROOT
==========================================================================
*sal1_h.lib file:*
!!index array str
"sal1_h"
!entry.sal1_h.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg
"C1'" "c" 0 1 131072 1 6 0.664700
"O1'" "o" 0 1 131072 2 8 -0.589000
"O2'" "oh" 0 1 131072 3 8 -0.597100
"C1" "ca" 0 1 131072 4 6 -0.234600
"C2" "ca" 0 1 131072 5 6 0.208100
"C3" "ca" 0 1 131072 6 6 -0.184000
"C4" "ca" 0 1 131072 7 6 -0.057000
"C5" "ca" 0 1 131072 8 6 -0.188000
"C6" "ca" 0 1 131072 9 6 -0.033000
"O2" "oh" 0 1 131072 10 8 -0.498100
"HO2'" "ho" 0 1 131072 11 1 0.451000
"HO2" "ho" 0 1 131072 12 1 0.461000
"H6" "ha" 0 1 131072 13 1 0.156000
"H5" "ha" 0 1 131072 14 1 0.142000
"H4" "ha" 0 1 131072 15 1 0.140000
"H3" "ha" 0 1 131072 16 1 0.158000
!entry.sal1_h.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
"C1'" "c" 0 -1 0.0
"O1'" "o" 0 -1 0.0
"O2'" "oh" 0 -1 0.0
"C1" "ca" 0 -1 0.0
"C2" "ca" 0 -1 0.0
"C3" "ca" 0 -1 0.0
"C4" "ca" 0 -1 0.0
"C5" "ca" 0 -1 0.0
"C6" "ca" 0 -1 0.0
"O2" "oh" 0 -1 0.0
"HO2'" "ho" 0 -1 0.0
"HO2" "ho" 0 -1 0.0
"H6" "ha" 0 -1 0.0
"H5" "ha" 0 -1 0.0
"H4" "ha" 0 -1 0.0
"H3" "ha" 0 -1 0.0
!entry.sal1_h.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.sal1_h.unit.childsequence single int
2
!entry.sal1_h.unit.connect array int
0
0
!entry.sal1_h.unit.connectivity table int atom1x int atom2x int flags
1 2 2
1 3 1
1 4 1
3 11 1
4 5 4
4 9 4
5 6 4
5 10 1
6 7 4
6 16 1
7 8 4
7 15 1
8 9 4
8 14 1
9 13 1
10 12 1
!entry.sal1_h.unit.hierarchy table str abovetype int abovex str belowtype
int belowx
"U" 0 "R" 1
"R" 1 "A" 1
"R" 1 "A" 2
"R" 1 "A" 3
"R" 1 "A" 4
"R" 1 "A" 5
"R" 1 "A" 6
"R" 1 "A" 7
"R" 1 "A" 8
"R" 1 "A" 9
"R" 1 "A" 10
"R" 1 "A" 11
"R" 1 "A" 12
"R" 1 "A" 13
"R" 1 "A" 14
"R" 1 "A" 15
"R" 1 "A" 16
!entry.sal1_h.unit.name single str
"SAL"
!entry.sal1_h.unit.positions table dbl x dbl y dbl z
31.071000 2.749000 30.834000
30.339000 2.130000 31.722000
31.484000 3.937000 31.173000
31.430000 2.169000 29.525000
31.001000 0.823000 29.065000
31.391000 0.264000 27.724000
32.221000 1.083000 26.849000
32.677000 2.428000 27.245000
32.269000 2.945000 28.582000
30.190000 -0.026000 29.863000
31.594000 3.981000 32.166000
29.988000 0.426000 30.732000
32.606000 3.948000 28.882000
33.302000 3.034000 26.572000
32.515000 0.686000 25.866000
31.058000 -0.737000 27.412000
!entry.sal1_h.unit.residueconnect table int c1x int c2x int c3x int c4x
int c5x int c6x
0 0 0 0 0 0
!entry.sal1_h.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
"SAL" 1 17 1 "?" 0
!entry.sal1_h.unit.residuesPdbSequenceNumber array int
0
!entry.sal1_h.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.sal1_h.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
==========================================================================
*sal1_h.inpcrd file:*
SAL
16
31.0710000 2.7490000 30.8340000 30.3390000 2.1300000 31.7220000
31.4840000 3.9370000 31.1730000 31.4300000 2.1690000 29.5250000
31.0010000 0.8230000 29.0650000 31.3910000 0.2640000 27.7240000
32.2210000 1.0830000 26.8490000 32.6770000 2.4280000 27.2450000
32.2690000 2.9450000 28.5820000 30.1900000 -0.0260000 29.8630000
31.5940000 3.9810000 32.1660000 29.9880000 0.4260000 30.7320000
32.6060000 3.9480000 28.8820000 33.3020000 3.0340000 26.5720000
32.5150000 0.6860000 25.8660000 31.0580000 -0.7370000 27.4120000
==========================================================================
*sal1_h.prmtop file:*
%VERSION VERSION_STAMP = V0001.000 DATE = 12/08/14 22:08:00
%FLAG TITLE
%FORMAT(20a4)
SAL
%FLAG POINTERS
%FORMAT(10I8)
16 5 6 10 10 13 22 18 0
0
71 1 10 13 18 7 9 6 6
0
0 0 0 0 0 0 0 0 16
0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
C1' O1' O2' C1 C2 C3 C4 C5 C6 O2 HO2'HO2 H6 H5 H4 H3
%FLAG CHARGE
%FORMAT(5E16.8)
1.21123628E+01 -1.07329347E+01 -1.08805353E+01 -4.27495158E+00
3.79206063E+00
-3.35290320E+00 -1.03867110E+00 -3.42579240E+00 -6.01335900E-01
-9.07652763E+00
8.21825730E+00 8.40048030E+00 2.84267880E+00 2.58756660E+00
2.55112200E+00
2.87912340E+00
%FLAG MASS
%FORMAT(5E16.8)
1.20100000E+01 1.60000000E+01 1.60000000E+01 1.20100000E+01
1.20100000E+01
1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01
1.60000000E+01
1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00
1.00800000E+00
1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 3 1 1 1 1 1 1
3
4 4 5 5 5 5
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
10 5 4 11 9 8 7 5 4
2
1 1 1 1 1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 4 7 11 2 3 5 8
12
4 5 6 9 13 7 8 9 10
14
11 12 13 14 15
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
SAL
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
6.48000000E+02 4.66400000E+02 3.49700000E+02 3.69600000E+02
4.78400000E+02
3.86100000E+02 3.44300000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.21400000E+00 1.30600000E+00 1.48700000E+00 9.74000000E-01
1.38700000E+00
1.36200000E+00 1.08700000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
5.11900000E+01 6.46400000E+01 7.73800000E+01 6.86700000E+01
7.01100000E+01
6.71800000E+01 6.98500000E+01 4.84600000E+01 4.88500000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
1.87396082E+00 2.09683946E+00 2.14466150E+00 2.15443535E+00
1.97990235E+00
2.09387240E+00 2.09334880E+00 2.09457053E+00 1.91061275E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
3.62500000E+00 1.90000000E+00 2.30000000E+00 9.00000000E-01
1.05000000E+01
1.10000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
2.00000000E+00 1.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00
2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
3.14159400E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00
3.14159400E+00
3.14159400E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
8.19971662E+05 5.74393458E+05 3.79876399E+05 7.01803794E+05
4.71003287E+05
5.81803229E+05 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
7.62451550E+04 4.77908183E+04 6.00750218E+04 0.00000000E+00
5.71629601E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
5.31102864E+02 5.55666448E+02 5.64885984E+02 6.14502845E+02
6.29300710E+02
6.99746810E+02 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
1.04660679E+02 1.03580945E+02 1.16187983E+02 0.00000000E+00
1.85196588E+01
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
6 30 4 15 45 7 18 42 7
21
39 7 24 36 7 27 33 4
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 3 1 0 6 2 0 9 3
9
12 5 9 24 5 12 15 5 12
27
6 15 18 5 18 21 5 21 24
5
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
0 6 30 1 9 24 36 8 12
15
45 8 12 27 33 9 15 18 42
8
18 15 45 8 18 21 39 8 21
18
42 8 21 24 36 8 24 21 39
8
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 9 12 2 0 9 24 2 3
0
6 3 3 0 9 4 6 0 9
5
9 12 15 6 9 12 27 7 9
24
21 6 12 9 24 6 12 15 18
6
15 12 27 7 15 18 21 6 18
21
24 6
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
0 9 24 36 1 3 0 6 30
2
3 0 -6 30 3 9 0 6 30
3
9 12 15 45 1 9 12 27 33
4
9 24 21 39 1 12 9 24 36
1
12 15 18 42 1 15 12 27 33
4
15 18 21 39 1 18 21 24 36
1
21 18 15 45 1 24 21 18 42
1
27 12 15 45 1 36 24 21 39
1
39 21 18 42 1 42 18 15 45
1
12 18 -15 -45 6 15 21 -18 -42
6
18 24 -21 -39 6 9 21 -24 -36
6
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 9 12 15 1 0 9 12 27
1
0 9 24 21 1 3 0 9 12
1
3 0 9 24 1 6 0 9 12
1
6 0 9 24 1 9 12 15 18
1
9 24 -21 18 1 12 9 24 21
1
12 15 -18 21 1 15 12 9 24
1
15 18 -21 24 1 18 15 12 27
1
24 9 12 27 1 6 0 -3 -9
5
0 12 -9 -24 6 9 15 -12 -27
6
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 8 9 10 11
13
3 4 5 9 11 4 5 9 11
5
6 7 8 9 10 11 12 13 14
16
6 7 8 9 10 12 13 15 16
7
8 9 10 12 14 15 16 8 9
10
13 14 15 16 9 13 14 15 16
10
13 14 15 12 16 0 0 14 15
16
0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
c o oh ca ca ca ca ca ca oh ho ho ha ha ha ha
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0
0
0 0 0 0 0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0
0
0 0 0 0 0 0
%FLAG RADIUS_SET
%FORMAT(1a80)
modified Bondi radii (mbondi)
%FLAG RADII
%FORMAT(5E16.8)
1.70000000E+00 1.50000000E+00 1.50000000E+00 1.70000000E+00
1.70000000E+00
1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00
1.50000000E+00
8.00000000E-01 8.00000000E-01 1.30000000E+00 1.30000000E+00
1.30000000E+00
1.30000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
7.20000000E-01
7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01
8.50000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
8.50000000E-01
8.50000000E-01
==========================================================================
*For making prmtop and inpcrd files for complex, I used following commands:*
$AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03
source leaprc.gaff
loadamberparams sal1_h.frcmod
loadoff sal1_h.lib
comp1 = loadpdb comp1.pdb
*Loading PDB file: ./comp1.pdb*
*Unknown residue: SAL number: 97 type: Terminal/last*
*..relaxing end constraints to try for a dbase match*
* -no luck*
* Added missing heavy atom: .R<CGLN 204>.A<OXT 18>*
*Creating new UNIT for residue: SAL sequence: 205*
*Created a new atom named: C1' within residue: .R<SAL 205>*
*Created a new atom named: O1' within residue: .R<SAL 205>*
*Created a new atom named: O2' within residue: .R<SAL 205>*
*Created a new atom named: C1 within residue: .R<SAL 205>*
*Created a new atom named: C2 within residue: .R<SAL 205>*
*Created a new atom named: C3 within residue: .R<SAL 205>*
*Created a new atom named: C4 within residue: .R<SAL 205>*
*Created a new atom named: C5 within residue: .R<SAL 205>*
*Created a new atom named: C6 within residue: .R<SAL 205>*
*Created a new atom named: O2 within residue: .R<SAL 205>*
* total atoms in file: 798*
* Leap added 788 missing atoms according to residue templates:*
* 1 Heavy*
* 785 H / lone pairs*
* 2 unknown element*
****** The file contained 10 atoms not in residue templates*
*Unknown element? I don’t know.*
addions comp1 Cl- 0
saveamberparams comp1 comp1.prmtop comp1.inpcrd
*Checking Unit.*
*FATAL: Atom .R<SAL 205>.A<C1' 1> does not have a type.*
*FATAL: Atom .R<SAL 205>.A<O1' 2> does not have a type.*
*FATAL: Atom .R<SAL 205>.A<O2' 3> does not have a type.*
*FATAL: Atom .R<SAL 205>.A<C1 4> does not have a type.*
*FATAL: Atom .R<SAL 205>.A<C2 5> does not have a type.*
*FATAL: Atom .R<SAL 205>.A<C3 6> does not have a type.*
*FATAL: Atom .R<SAL 205>.A<C4 7> does not have a type.*
*FATAL: Atom .R<SAL 205>.A<C5 8> does not have a type.*
*FATAL: Atom .R<SAL 205>.A<C6 9> does not have a type.*
*FATAL: Atom .R<SAL 205>.A<O2 10> does not have a type.*
*Failed to generate parameters*
*Parameter file was not saved.*
==========================================================================
*How to solve this problem?*
*Any help will highly appreciated.*
*Best wishes,*
*Atila*
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Received on Mon Dec 08 2014 - 23:00:02 PST
