Hi all,
You were of course right.. as usual helpful tips!
Just an addition point that can be useful to be discussed.
Do you have any reason why I am not able to correctly recognize my ligand
why it seems I am calling it correctly?
Antonios-MacBook-Air:4U6R_plus_kira Antonio$ *cat kira.pdb*
HEADER TRANSFERASE/TRANSFERASE INHIBITOR
REMARK 99
REMARK 99 MOE v2018.01 (Chemical Computing Group ULC) Wed Oct 03 07:58:53
2018
HETATM 1 C21 *3E4* 1 -5.809 -25.013 -1.347 1.00 28.83
C
HETATM 2 C22 3E4 1 -6.027 -26.352 -1.984 1.00 28.29
C
HETATM 3 C23 3E4 1 -5.825 -26.262 -3.449 1.00 29.90
C
HETATM 4 N6 3E4 1 -5.846 -27.585 -3.996 1.00 30.56
N1+
HETATM 5 C24 3E4 1 -4.499 -25.634 -3.790 1.00 29.33
C
HETATM 6 C25 3E4 1 -4.231 -24.356 -3.050 1.00 29.07
C
HETATM 7 C20 3E4 1 -4.417 -24.526 -1.568 1.00 28.65
C
HETATM 8 N4 3E4 1 -4.235 -23.289 -0.849 1.00 29.41
N
HETATM 9 C12 3E4 1 -3.075 -22.799 -0.595 1.00 28.33
C
HETATM 10 N2 3E4 1 -2.049 -23.578 -0.564 1.00 27.26
N
HETATM 11 N3 3E4 1 -2.951 -21.519 -0.367 1.00 28.51
N
HETATM 12 C15 3E4 1 -1.802 -20.987 -0.118 1.00 27.41
C
HETATM 13 C13 3E4 1 -0.707 -21.795 -0.075 1.00 28.17
C
HETATM 14 C11 3E4 1 -0.861 -23.129 -0.321 1.00 28.55
C
HETATM 15 C14 3E4 1 0.159 -24.050 -0.268 1.00 29.20
C
HETATM 16 C16 3E4 1 -0.225 -25.351 -0.151 1.00 29.51
C
HETATM 17 C17 3E4 1 0.709 -26.329 -0.071 1.00 30.25
C
HETATM 18 C18 3E4 1 2.004 -25.949 -0.090 1.00 29.15
C
HETATM 19 N5 3E4 1 2.353 -24.704 -0.180 1.00 31.20
N
HETATM 20 C19 3E4 1 1.490 -23.733 -0.262 1.00 30.43
C
HETATM 21 O1 3E4 1 1.878 -22.456 -0.368 1.00 33.20
O
HETATM 22 C4 3E4 1 3.082 -22.014 -0.053 1.00 32.88
C
HETATM 23 C5 3E4 1 4.067 -21.896 -0.986 1.00 33.33
C
HETATM 24 C26 3E4 1 3.877 -22.331 -2.400 1.00 31.42
C
HETATM 25 C6 3E4 1 5.291 -21.432 -0.635 1.00 35.10
C
HETATM 26 C3 3E4 1 3.320 -21.591 1.202 1.00 32.48
C
HETATM 27 C10 3E4 1 2.331 -21.678 2.130 1.00 32.06
C
HETATM 28 C9 3E4 1 2.539 -21.287 3.422 1.00 30.89
C
HETATM 29 C8 3E4 1 3.752 -20.783 3.782 1.00 31.14
C
HETATM 30 C7 3E4 1 4.752 -20.693 2.849 1.00 32.17
C
HETATM 31 C2 3E4 1 4.538 -21.102 1.562 1.00 33.82
C
HETATM 32 C1 3E4 1 5.537 -21.021 0.633 1.00 36.52
C
HETATM 33 N1 3E4 1 6.707 -20.546 0.921 1.00 41.72
N
HETATM 34 S1 3E4 1 7.174 -19.117 0.354 1.00 51.09
S2+
HETATM 35 O2 3E4 1 6.399 -18.653 -0.786 1.00 47.06
O1-
HETATM 36 O3 3E4 1 8.558 -19.217 0.080 1.00 51.10
O1-
HETATM 37 C27 3E4 1 6.924 -17.844 1.373 1.00 52.56
C
HETATM 38 C32 3E4 1 5.965 -16.970 0.938 1.00 52.06
C
HETATM 39 C31 3E4 1 5.680 -15.873 1.712 1.00 52.33
C
HETATM 40 C30 3E4 1 6.331 -15.660 2.902 1.00 52.15
C
HETATM 41 C29 3E4 1 7.283 -16.528 3.332 1.00 52.63
C
HETATM 42 C28 3E4 1 7.572 -17.606 2.566 1.00 53.23
C
HETATM 43 CL1 3E4 1 8.756 -18.621 3.183 1.00 63.38
CL
HETATM 44 H211 3E4 1 -6.003 -25.106 -0.276 1.00 0.00
H
HETATM 45 H212 3E4 1 -6.547 -24.299 -1.723 1.00 0.00
H
HETATM 46 H221 3E4 1 -7.038 -26.701 -1.763 1.00 0.00
H
HETATM 47 H222 3E4 1 -5.350 -27.082 -1.531 1.00 0.00
H
HETATM 48 H23 3E4 1 -6.644 -25.730 -3.935 1.00 0.00
H
HETATM 49 H61 3E4 1 -5.625 -27.571 -4.992 1.00 0.00
H
HETATM 50 H62 3E4 1 -5.157 -28.164 -3.539 1.00 0.00
H
HETATM 51 H63 3E4 1 -6.757 -28.004 -3.878 1.00 0.00
H
HETATM 52 H241 3E4 1 -4.438 -25.453 -4.864 1.00 0.00
H
HETATM 53 H242 3E4 1 -3.683 -26.327 -3.568 1.00 0.00
H
HETATM 54 H251 3E4 1 -4.892 -23.573 -3.430 1.00 0.00
H
HETATM 55 H252 3E4 1 -3.216 -24.021 -3.270 1.00 0.00
H
HETATM 56 H20 3E4 1 -3.717 -25.275 -1.190 1.00 0.00
H
HETATM 57 HN4 3E4 1 -4.988 -22.619 -0.927 1.00 0.00
H
HETATM 58 H15 3E4 1 -1.755 -19.925 0.078 1.00 0.00
H
HETATM 59 H13 3E4 1 0.190 -21.282 0.210 1.00 0.00
H
HETATM 60 H16 3E4 1 -1.245 -25.705 -0.109 1.00 0.00
H
HETATM 61 H17 3E4 1 0.428 -27.368 0.017 1.00 0.00
H
HETATM 62 H18 3E4 1 2.800 -26.677 -0.025 1.00 0.00
H
HETATM 63 H261 3E4 1 4.757 -22.175 -3.020 1.00 0.00
H
HETATM 64 H262 3E4 1 3.639 -23.394 -2.440 1.00 0.00
H
HETATM 65 H263 3E4 1 3.050 -21.784 -2.854 1.00 0.00
H
HETATM 66 H6 3E4 1 6.080 -21.413 -1.367 1.00 0.00
H
HETATM 67 H10 3E4 1 1.358 -22.078 1.893 1.00 0.00
H
HETATM 68 H9 3E4 1 1.748 -21.369 4.153 1.00 0.00
H
HETATM 69 H8 3E4 1 3.916 -20.451 4.796 1.00 0.00
H
HETATM 70 H7 3E4 1 5.701 -20.287 3.168 1.00 0.00
H
HETATM 71 HN1 3E4 1 6.936 -20.616 1.900 1.00 0.00
H
HETATM 72 H32 3E4 1 5.327 -17.021 0.069 1.00 0.00
H
HETATM 73 H31 3E4 1 4.892 -15.210 1.392 1.00 0.00
H
HETATM 74 H30 3E4 1 6.093 -14.789 3.493 1.00 0.00
H
HETATM 75 H29 3E4 1 7.796 -16.349 4.266 1.00 0.00
H
END
> source leaprc.gaff
----- Source: /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.gaff
----- Source of /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /Users/Antonio/Desktop/amber18/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
> *3E4 = loadmol2 kira.mol2*
Error: Error from the parser: syntax error
> *3E4=loadmol2 kira.mol2 *
Error: Error from the parser: syntax error
> *3E4 = loadmol2 kira.mol2*
Error: Error from the parser: syntax error
> *1 = loadmol2 kira.mol2 *
Error: Error from the parser: syntax error
> *A1001 = loadmol2 kira.mol2*
Loading Mol2 file: ./kira.mol2
Reading MOLECULE named 3E4
If someone interested, the overall procedure with the final aim to
correctly prepare a protein-ligand MD simulations is enclosed..
Antonios-MacBook-Air:4U6R_plus_kira Antonio$ *antechamber -i kira.pdb -fi
pdb -o kira.mol2 -fo mol2 -c bcc -s 2 -nc 1*
Welcome to antechamber 17.3: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
Status: pass
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Status: pass
-- Check Geometry --
for those bonded
for those not bonded
Status: pass
-- Check Weird Bonds --
Status: pass
-- Check Number of Units --
Status: pass
acdoctor mode has completed checking the input file.
Running: /Users/Antonio/Desktop/amber18/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /Users/Antonio/Desktop/amber18/bin/atomtype -i ANTECHAMBER_AC.AC0
-o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 322; net charge: 1
Running: /Users/Antonio/Desktop/amber18/bin/sqm -O -i sqm.in -o sqm.out
Running: /Users/Antonio/Desktop/amber18/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Users/Antonio/Desktop/amber18/dat/antechamber/BCCPARM.DAT -s 2 -j 1
Running: /Users/Antonio/Desktop/amber18/bin/atomtype -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
Antonios-MacBook-Air:4U6R_plus_kira Antonio$ *cat kira.mol2*
.<TRIPOS>MOLECULE
3E4
75 80 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 C21 -5.8090 -25.0130 -1.3470 c3 1 3E4
-0.102400
2 C22 -6.0270 -26.3520 -1.9840 c3 1 3E4
-0.096900
3 C23 -5.8250 -26.2620 -3.4490 c3 1 3E4
0.115500
4 N6 -5.8460 -27.5850 -3.9960 n4 1 3E4
-0.843600
5 C24 -4.4990 -25.6340 -3.7900 c3 1 3E4
-0.096900
6 C25 -4.2310 -24.3560 -3.0500 c3 1 3E4
-0.102400
7 C20 -4.4170 -24.5260 -1.5680 c3 1 3E4
0.206500
8 N4 -4.2350 -23.2890 -0.8490 nh 1 3E4
-0.807900
9 C12 -3.0750 -22.7990 -0.5950 ca 1 3E4
0.835900
10 N2 -2.0490 -23.5780 -0.5640 nb 1 3E4
-0.752000
11 N3 -2.9510 -21.5190 -0.3670 nb 1 3E4
-0.729000
12 C15 -1.8020 -20.9870 -0.1180 ca 1 3E4
0.461200
13 C13 -0.7070 -21.7950 -0.0750 ca 1 3E4
-0.359600
14 C11 -0.8610 -23.1290 -0.3210 cp 1 3E4
0.542800
15 C14 0.1590 -24.0500 -0.2680 cp 1 3E4
-0.303800
16 C16 -0.2250 -25.3510 -0.1510 ca 1 3E4
-0.035000
17 C17 0.7090 -26.3290 -0.0710 ca 1 3E4
-0.290300
18 C18 2.0040 -25.9490 -0.0900 ca 1 3E4
0.448200
19 N5 2.3530 -24.7040 -0.1800 nb 1 3E4
-0.701000
20 C19 1.4900 -23.7330 -0.2620 ca 1 3E4
0.645600
21 O1 1.8780 -22.4560 -0.3680 os 1 3E4
-0.370400
22 C4 3.0820 -22.0140 -0.0530 ca 1 3E4
0.078100
23 C5 4.0670 -21.8960 -0.9860 ca 1 3E4
-0.034300
24 C26 3.8770 -22.3310 -2.4000 c3 1 3E4
-0.052800
25 C6 5.2910 -21.4320 -0.6350 ca 1 3E4
-0.171000
26 C3 3.3200 -21.5910 1.2020 ca 1 3E4
-0.009000
27 C10 2.3310 -21.6780 2.1300 ca 1 3E4
-0.118000
28 C9 2.5390 -21.2870 3.4220 ca 1 3E4
-0.114000
29 C8 3.7520 -20.7830 3.7820 ca 1 3E4
-0.123000
30 C7 4.7520 -20.6930 2.8490 ca 1 3E4
-0.116000
31 C2 4.5380 -21.1020 1.5620 ca 1 3E4
-0.048000
32 C1 5.5370 -21.0210 0.6330 ca 1 3E4
0.187600
33 N1 6.7070 -20.5460 0.9210 nh 1 3E4
-0.777500
34 S1 7.1740 -19.1170 0.3540 sy 1 3E4
1.512200
35 O2 6.3990 -18.6530 -0.7860 o 1 3E4
-0.641300
36 O3 8.5580 -19.2170 0.0800 o 1 3E4
-0.641300
37 C27 6.9240 -17.8440 1.3730 ca 1 3E4
-0.370500
38 C32 5.9650 -16.9700 0.9380 ca 1 3E4
-0.019000
39 C31 5.6800 -15.8730 1.7120 ca 1 3E4
-0.153000
40 C30 6.3310 -15.6600 2.9020 ca 1 3E4
-0.056000
41 C29 7.2830 -16.5280 3.3320 ca 1 3E4
-0.149000
42 C28 7.5720 -17.6060 2.5660 ca 1 3E4
0.130400
43 CL1 8.7560 -18.6210 3.1830 cl 1 3E4
-0.079400
44 H211 -6.0030 -25.1060 -0.2760 hc 1 3E4
0.077700
45 H212 -6.5470 -24.2990 -1.7230 hc 1 3E4
0.077700
46 H221 -7.0380 -26.7010 -1.7630 hc 1 3E4
0.069200
47 H222 -5.3500 -27.0820 -1.5310 hc 1 3E4
0.069200
48 H23 -6.6440 -25.7300 -3.9350 hx 1 3E4
0.111700
49 H61 -5.6250 -27.5710 -4.9920 hn 1 3E4
0.458133
50 H62 -5.1570 -28.1640 -3.5390 hn 1 3E4
0.458133
51 H63 -6.7570 -28.0040 -3.8780 hn 1 3E4
0.458133
52 H241 -4.4380 -25.4530 -4.8640 hc 1 3E4
0.069200
53 H242 -3.6830 -26.3270 -3.5680 hc 1 3E4
0.069200
54 H251 -4.8920 -23.5730 -3.4300 hc 1 3E4
0.077700
55 H252 -3.2160 -24.0210 -3.2700 hc 1 3E4
0.077700
56 H20 -3.7170 -25.2750 -1.1900 h1 1 3E4
0.092700
57 HN4 -4.9880 -22.6190 -0.9270 hn 1 3E4
0.419800
58 H15 -1.7550 -19.9250 0.0780 h4 1 3E4
0.041100
59 H13 0.1900 -21.2820 0.2100 ha 1 3E4
0.175000
60 H16 -1.2450 -25.7050 -0.1090 ha 1 3E4
0.152000
61 H17 0.4280 -27.3680 0.0170 ha 1 3E4
0.153000
62 H18 2.8000 -26.6770 -0.0250 h4 1 3E4
0.036100
63 H261 4.7570 -22.1750 -3.0200 hc 1 3E4
0.049367
64 H262 3.6390 -23.3940 -2.4400 hc 1 3E4
0.049367
65 H263 3.0500 -21.7840 -2.8540 hc 1 3E4
0.049367
66 H6 6.0800 -21.4130 -1.3670 ha 1 3E4
0.177000
67 H10 1.3580 -22.0780 1.8930 ha 1 3E4
0.135000
68 H9 1.7480 -21.3690 4.1530 ha 1 3E4
0.139000
69 H8 3.9160 -20.4510 4.7960 ha 1 3E4
0.141000
70 H7 5.7010 -20.2870 3.1680 ha 1 3E4
0.135000
71 HN1 6.9360 -20.6160 1.9000 hn 1 3E4
0.462800
72 H32 5.3270 -17.0210 0.0690 ha 1 3E4
0.169000
73 H31 4.8920 -15.2100 1.3920 ha 1 3E4
0.148000
74 H30 6.0930 -14.7890 3.4930 ha 1 3E4
0.147000
75 H29 7.7960 -16.3490 4.2660 ha 1 3E4
0.159000
.<TRIPOS>BOND
1 1 2 1
2 1 7 1
3 1 44 1
4 1 45 1
5 2 3 1
6 2 46 1
7 2 47 1
8 3 4 1
9 3 5 1
10 3 48 1
11 4 49 1
12 4 50 1
13 4 51 1
14 5 6 1
15 5 52 1
16 5 53 1
17 6 7 1
18 6 54 1
19 6 55 1
20 7 8 1
21 7 56 1
22 8 9 1
23 8 57 1
24 9 10 ar
25 9 11 ar
26 10 14 ar
27 11 12 ar
28 12 13 ar
29 12 58 1
30 13 14 ar
31 13 59 1
32 14 15 1
33 15 16 ar
34 15 20 ar
35 16 17 ar
36 16 60 1
37 17 18 ar
38 17 61 1
39 18 19 ar
40 18 62 1
41 19 20 ar
42 20 21 1
43 21 22 1
44 22 23 ar
45 22 26 ar
46 23 24 1
47 23 25 ar
48 24 63 1
49 24 64 1
50 24 65 1
51 25 32 ar
52 25 66 1
53 26 27 ar
54 26 31 ar
55 27 28 ar
56 27 67 1
57 28 29 ar
58 28 68 1
59 29 30 ar
60 29 69 1
61 30 31 ar
62 30 70 1
63 31 32 ar
64 32 33 1
65 33 34 1
66 33 71 1
67 34 35 2
68 34 36 2
69 34 37 1
70 37 38 ar
71 37 42 ar
72 38 39 ar
73 38 72 1
74 39 40 ar
75 39 73 1
76 40 41 ar
77 40 74 1
78 41 42 ar
79 41 75 1
80 42 43 1
.<TRIPOS>SUBSTRUCTURE
1 3E4 1 TEMP 0 **** **** 0 ROOT
Antonios-MacBook-Air:4U6R_plus_kira Antonio$ *parmchk2 -i kira.mol2 -f mol2
-o kira.frcmod*
Antonios-MacBook-Air:4U6R_plus_kira Antonio$ *cat kira.frcmod*
Remark line goes here
MASS
BOND
ANGLE
DIHE
ca-cp-nb-ca 2 9.600 180.000 2.000 same as X
-ca-nb-X , penalty score=418.5
cp-cp-nb-ca 2 9.600 180.000 2.000 same as X
-ca-nb-X , penalty score=418.5
IMPROPER
c3-ca-nh-hn 1.1 180.0 2.0 Same as X -X
-na-hn, penalty score= 41.2 (use general term))
nb-nb-ca-nh 10.5 180.0 2.0 Same as X
-n2-ca-n2, penalty score= 48.6 (use general term))
ca-h4-ca-nb 1.1 180.0 2.0 Same as X -X
-ca-ha, penalty score= 44.3 (use general term))
ca-cp-ca-ha 1.1 180.0 2.0 Using general
improper torsional angle X- X-ca-ha, penalty score= 6.0)
ca-cp-cp-nb 1.1 180.0 2.0 Using the
default value
ca-ca-cp-cp 1.1 180.0 2.0 Same as
c2-ca-ca-ca, penalty score=309.7)
ca-ca-ca-ha 1.1 180.0 2.0 Using general
improper torsional angle X- X-ca-ha, penalty score= 6.0)
cp-nb-ca-os 1.1 180.0 2.0 Using the
default value
ca-ca-ca-os 1.1 180.0 2.0 Using the
default value
ca-ca-ca-ca 1.1 180.0 2.0 Same as
c2-ca-ca-ca, penalty score= 31.1)
ca-ca-ca-nh 1.1 180.0 2.0 Using the
default value
ca-hn-nh-sy 1.1 180.0 2.0 Same as X -X
-na-hn, penalty score= 41.2 (use general term))
ca-ca-ca-sy 1.1 180.0 2.0 Using the
default value
NONBON
Antonios-MacBook-Air:4U6R_plus_kira Antonio$ *tleap*
-I: Adding /Users/Antonio/Desktop/amber18/dat/leap/prep to search path.
-I: Adding /Users/Antonio/Desktop/amber18/dat/leap/lib to search path.
-I: Adding /Users/Antonio/Desktop/amber18/dat/leap/parm to search path.
-I: Adding /Users/Antonio/Desktop/amber18/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> *source leaprc.ff14SB*
----- Source: /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.ff14SB
----- Source of /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.ff14SB
done
Log file: ./leap.log
Loading parameters: /Users/Antonio/Desktop/amber18/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters:
/Users/Antonio/Desktop/amber18/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/amino12.lib
Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/aminoct12.lib
Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/aminont12.lib
Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/nucleic12.lib
Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/atomic_ions.lib
Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/solvents.lib
> *source leaprc.gaff*
----- Source: /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.gaff
----- Source of /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /Users/Antonio/Desktop/amber18/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
> *3E4 = loadmol2 kira.mol2*
Error: Error from the parser: syntax error
> *3E4=loadmol2 kira.mol2 *
Error: Error from the parser: syntax error
> *3E4 = loadmol2 kira.mol2*
Error: Error from the parser: syntax error
> *1 = loadmol2 kira.mol2 *
Error: Error from the parser: syntax error
> *A1001 = loadmol2 kira.mol2*
Loading Mol2 file: ./kira.mol2
Reading MOLECULE named 3E4
> *list*
A *A1001* A3 A5 ACE AG AL
ALA
AN ARG ASH ASN ASP Ag BA BR
Be C C3 C5 CA CALA CARG CASN
CASP CCYS CCYX CD CE CGLN CGLU CGLY
CHCL3BOX CHID CHIE CHIP CHIS CHYP CILE CL
CLEU CLYS CMET CN CO CPHE CPRO CR
CS CSER CTHR CTRP CTYR CU CU1 CVAL
CYM CYS CYX Ce Cl- Cr DA DA3
DA5 DAN DC DC3 DC4 DC5 DCN DG
DG3 DG5 DGN DT DT3 DT5 DTN Dy
EU EU3 Er F FB3 FB3BOX FB4
FB4BOX
FE FE2 G G3 G5 GD3 GLH GLN
GLU GLY GN H3O+ HE+ HG HID HIE
HIP HIS HOH HYP HZ+ Hf ILE IN
IOD K K+ LA LEU LI LU LYN
LYS MEOHBOX MET MG MN NA NALA NARG
NASN NASP NCYS NCYX NGLN NGLU NGLY NH4
NHE NHID NHIE NHIP NHIS NI NILE NLEU
NLYS NMABOX NME NMET NPHE NPRO NSER NTHR
NTRP NTYR NVAL Na+ Nd OHE OP3 OPC
OPC3BOX OPCBOX PB PD PHE PL3 POL3BOX PR
PRO PT Pu QSPCFWBOX RB Ra S2P SER
SM SPC SPCBOX SPCFWBOX SPF SPG SR Sm
Sn T2P T4E TB THR TIP3PBOX TIP3PFBOX
TIP4PBOX
TIP4PEWBOXTIP5PBOX TL TP3 TP4 TP5 TPF TRP
TYR Th Tl Tm U U3 U4+ U5
UN V2+ VAL WAT Y YB2 ZN Zr
frcmod14SBgaff parm10
> *loadamberparams kira.frcmod*
Loading parameters: ./kira.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> *check A1001*
Checking 'A1001'....
Warning: The unperturbed charge of the unit (1.004000) is not zero.
Checking parameters for unit 'A1001'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
> *saveoff A1001 a1001.lib*
Creating a1001.lib
Building topology.
Building atom parameters.
> *saveamberparm A1001 kira.prmtop kira.inpcrd*
Checking Unit.
Warning: The unperturbed charge of the unit (1.004000) is not zero.
Note: Ignoring the warning from Unit Checking.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 27 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
3E4 1
)
(no restraints)
> *loadoff a1001.lib*
Loading library: ./a1001.lib
> *complex = loadPDB 4u6r_prepared_2.pdb*
Loading PDB file: ./4u6r_prepared_2.pdb
Warning: Unknown residue: NMA number: 404 type: Terminal/last
..relaxing end constraints to try for a dbase match
Warning: -no luck
Warning: Unknown residue: 3E4 number: 405 type: Terminal/last
..relaxing end constraints to try for a dbase match
Warning: -no luck
Created a new atom named: HH31 within residue: .R<ACE 560>
Created a new atom named: HH32 within residue: .R<ACE 560>
Created a new atom named: HH33 within residue: .R<ACE 560>
Creating new UNIT for residue: NMA sequence: 964
Warning: One sided connection. Residue () missing connect0 atom.
Created a new atom named: N within residue: .R<NMA 964>
Created a new atom named: CA within residue: .R<NMA 964>
Created a new atom named: H within residue: .R<NMA 964>
Created a new atom named: HA1 within residue: .R<NMA 964>
Created a new atom named: HA2 within residue: .R<NMA 964>
Created a new atom named: HA3 within residue: .R<NMA 964>
Creating new UNIT for residue: 3E4 sequence: 965
Created a new atom named: C21 within residue: .R<3E4 965>
Created a new atom named: C22 within residue: .R<3E4 965>
Created a new atom named: C23 within residue: .R<3E4 965>
Created a new atom named: N6 within residue: .R<3E4 965>
Created a new atom named: C24 within residue: .R<3E4 965>
Created a new atom named: C25 within residue: .R<3E4 965>
Created a new atom named: C20 within residue: .R<3E4 965>
Created a new atom named: N4 within residue: .R<3E4 965>
Created a new atom named: C12 within residue: .R<3E4 965>
Created a new atom named: N2 within residue: .R<3E4 965>
Created a new atom named: N3 within residue: .R<3E4 965>
Created a new atom named: C15 within residue: .R<3E4 965>
Created a new atom named: C13 within residue: .R<3E4 965>
Created a new atom named: C11 within residue: .R<3E4 965>
Created a new atom named: C14 within residue: .R<3E4 965>
Created a new atom named: C16 within residue: .R<3E4 965>
Created a new atom named: C17 within residue: .R<3E4 965>
Created a new atom named: C18 within residue: .R<3E4 965>
Created a new atom named: N5 within residue: .R<3E4 965>
Created a new atom named: C19 within residue: .R<3E4 965>
Created a new atom named: O1 within residue: .R<3E4 965>
Created a new atom named: C4 within residue: .R<3E4 965>
Created a new atom named: C5 within residue: .R<3E4 965>
Created a new atom named: C26 within residue: .R<3E4 965>
Created a new atom named: C6 within residue: .R<3E4 965>
Created a new atom named: C3 within residue: .R<3E4 965>
Created a new atom named: C10 within residue: .R<3E4 965>
Created a new atom named: C9 within residue: .R<3E4 965>
Created a new atom named: C8 within residue: .R<3E4 965>
Created a new atom named: C7 within residue: .R<3E4 965>
Created a new atom named: C2 within residue: .R<3E4 965>
Created a new atom named: C1 within residue: .R<3E4 965>
Created a new atom named: N1 within residue: .R<3E4 965>
Created a new atom named: S1 within residue: .R<3E4 965>
Created a new atom named: O2 within residue: .R<3E4 965>
Created a new atom named: O3 within residue: .R<3E4 965>
Created a new atom named: C27 within residue: .R<3E4 965>
Created a new atom named: C32 within residue: .R<3E4 965>
Created a new atom named: C31 within residue: .R<3E4 965>
Created a new atom named: C30 within residue: .R<3E4 965>
Created a new atom named: C29 within residue: .R<3E4 965>
Created a new atom named: C28 within residue: .R<3E4 965>
Created a new atom named: CL1 within residue: .R<3E4 965>
Created a new atom named: H211 within residue: .R<3E4 965>
Created a new atom named: H212 within residue: .R<3E4 965>
Created a new atom named: H221 within residue: .R<3E4 965>
Created a new atom named: H222 within residue: .R<3E4 965>
Created a new atom named: H23 within residue: .R<3E4 965>
Created a new atom named: H61 within residue: .R<3E4 965>
Created a new atom named: H62 within residue: .R<3E4 965>
Created a new atom named: H63 within residue: .R<3E4 965>
Created a new atom named: H241 within residue: .R<3E4 965>
Created a new atom named: H242 within residue: .R<3E4 965>
Created a new atom named: H251 within residue: .R<3E4 965>
Created a new atom named: H252 within residue: .R<3E4 965>
Created a new atom named: H20 within residue: .R<3E4 965>
Created a new atom named: HN4 within residue: .R<3E4 965>
Created a new atom named: H15 within residue: .R<3E4 965>
Created a new atom named: H13 within residue: .R<3E4 965>
Created a new atom named: H16 within residue: .R<3E4 965>
Created a new atom named: H17 within residue: .R<3E4 965>
Created a new atom named: H18 within residue: .R<3E4 965>
Created a new atom named: H261 within residue: .R<3E4 965>
Created a new atom named: H262 within residue: .R<3E4 965>
Created a new atom named: H263 within residue: .R<3E4 965>
Created a new atom named: H6 within residue: .R<3E4 965>
Created a new atom named: H10 within residue: .R<3E4 965>
Created a new atom named: H9 within residue: .R<3E4 965>
Created a new atom named: H8 within residue: .R<3E4 965>
Created a new atom named: H7 within residue: .R<3E4 965>
Created a new atom named: HN1 within residue: .R<3E4 965>
Created a new atom named: H32 within residue: .R<3E4 965>
Created a new atom named: H31 within residue: .R<3E4 965>
Created a new atom named: H30 within residue: .R<3E4 965>
Created a new atom named: H29 within residue: .R<3E4 965>
total atoms in file: 6591
Leap added 3 missing atoms according to residue templates:
3 H / lone pairs
The file contained 84 atoms not in residue templates
> quit
Quit
Exiting LEaP: Errors = 6; Warnings = 7; Notes = 1.
On Tue, Oct 2, 2018 at 1:38 PM David Case <david.case.rutgers.edu> wrote:
> On Tue, Oct 02, 2018, Antonio Amber Carlesso wrote:
>
> > Welcome to LEaP!
> > (no leaprc in search path)
> > Sourcing: /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.ff14SB
>
> Above is quite odd: there should be no file called leaprc.ff14SB in the
> directory indicated. Did you perhaps untar AmberTools18 on top of some
> existing files? Or copy leaprc.ff14SB to this directory from somewhere
> else? Both can lead to problems. If you *really* need leaprc.ff14SB,
> look in the oldff folder.
>
> As Bill noted, you need to "source leaprc.gaff" to get the parameters
> used by antechamber.
>
> ...good luck....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Oct 03 2018 - 03:00:02 PDT
