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AMBER Archive (2009)
Subject: Re: [AMBER] COOH group troubling
From: Jio M (jiomm_at_yahoo.com)
Date: Sun Dec 06 2009 - 12:53:22 CST
- Previous message: Thomas Cheatham: "Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial"
- In reply to: Bill Ross: "Re: [AMBER] COOH group troubling"
- Next in thread: Bill Ross: "Re: [AMBER] COOH group troubling"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Dear AMBER users;
Thanks for reply,
I am giving ligand mol2 file and its frcmod file obtained by parmchk
>It would probably help us out if you included the frcmod that you're using
>so we don't have to guess at what's going on, along with your mol2 or prep
>file for the custom ligand.
Here is mol2 file
#####################################################
@<TRIPOS>MOLECULE
MOL
37 40 1 0 0
SMALL
resp
@<TRIPOS>ATOM
1
C1
3.5960 0.8310 -0.0240
cc 1
MOL 0.863085
2
C2
2.3150 1.2150 -0.0180
cd 1
MOL -0.965274
3
C3
1.2210 0.2500 -0.0190
cd 1
MOL 0.446138
4
C4
1.5960 -1.1680 -0.0170
cd 1
MOL -0.361520
5
C5
2.8710 -1.5870 -0.0200
cc 1
MOL 0.510971
6
C6
-0.0860 0.6000 -0.0330
cc 1
MOL 0.151491
7
C7 -0.7470
-1.7680 -0.0260
ca 1
MOL -0.196705
8
C8 -1.1330
-0.4210 -0.0310
ca 1
MOL 0.450403
9
C9 -2.4980
-0.1300 -0.0330
ca 1
MOL -0.836217
10
H1
-2.8230 0.8880 -0.0250
ha 1
MOL 0.214893
11
C10 -3.4410
-1.1420 -0.0350
ca 1
MOL 0.735201
12
C11 -3.0320
-2.4860 -0.0350
ca 1
MOL -0.310150
13
C12 -1.6710
-2.8050 -0.0270
ca 1
MOL 0.592792
14
H2
2.0640 2.2530 -0.0030
ha 1
MOL 0.259497
15
O1
0.5810 -2.0930 -0.0180
os 1
MOL -0.216186
16
I1
3.3850 -3.6220 -0.0210
i 1
MOL -0.068227
17
I2 -1.0530
-4.8140 -0.0220
i 1
MOL -0.064061
18
I3
5.1610 2.2450 -0.0200
i 1
MOL -0.102804
19
I4 -5.5020
-0.6230 -0.0380
i 1
MOL -0.034887
20
C13 3.9840
-0.6090 -0.0270
c 1
MOL 0.119328
21
O2
5.1570 -0.9550 -0.0350
o 1
MOL -0.654444
22
O3 -3.9020
-3.5290 -0.0370
oh 1
MOL -0.552747
23
H3 -4.8320
-3.3200 -0.0560
ho 1
MOL 0.303880
24
C14 -0.5070
2.0400 -0.0660 ca
1 MOL 0.043872
25
C15 -0.7190
2.6980 -1.2770 ca
1 MOL 0.205730
26
C16 -0.7240
2.7430 1.1200
ca 1
MOL -0.489797
27
C17 -1.1250
4.0280 -1.3140 ca
1 MOL 0.277710
28
C18 -1.1310
4.0700 1.0880
ca 1
MOL 0.319675
29
C19 -1.3300
4.7210 -0.1230 ca
1 MOL 0.148373
30
Cl1 -0.4610
1.8010 -2.7940 cl
1 MOL -0.295239
31
Cl2 -1.3800
4.8420 -2.8700 cl
1 MOL -0.221770
32
Cl3 -1.8430
6.4190 -0.1510 cl
1 MOL -0.187134
33
Cl4 -1.3730
4.9290 2.6300
cl 1
MOL -0.211557
34
C20 -0.5020
2.0540 2.4370
c 1
MOL 1.672474
35
O4
0.5780 1.8940 2.9560
o 1
MOL -1.009309
36
O5
-1.6600 1.6100 2.9680
oh 1
MOL -1.005568
37
H4
-1.5810 1.1910 3.8260
ho 1
MOL 0.468084
@<TRIPOS>BOND
1 1 2 2
2 1 18 1
3 1 20 1
4 2 3 1
5 2 14 1
6 3 4 ar
7 3 6 ar
8 4 5 2
9 4 15 ar
10 5 16 1
11 5 20 1
12 6 8 ar
13 6 24 1
14 7 8 ar
15 7 13 ar
16 7 15 ar
17 8 9 ar
18 9 10 1
19 9 11 ar
20 11 12 ar
21 11 19 1
22 12 13 ar
23 12 22 1
24 13 17 1
25 20 21 2
26 22 23 1
27 24 25 ar
28 24 26 ar
29 25 27 ar
30 25 30 1
31 26 28 ar
32 26 34 1
33 27 29 ar
34 27 31 1
35 28 29 ar
36 28 33 1
37 29 32 1
38 34 35 2
39 34 36 1
40 36 37 1
@<TRIPOS>SUBSTRUCTURE
1
MOL 1
TEMP
0 **** **** 0 ROOT
##################################################################
here is frcmod obtained for this mol2 by parmchk
remark goes here
MASS
BOND
cc-i 223.20 2.153 same as c2-i
ANGLE
cd-cc-i 56.300 121.030 same as c2-c2-i
ca-cc-ca 63.800 117.930 same as ca-ce-ca
i -cc-c 20.403 118.410 Calculated with empirical approach
DIHE
cd-cd-os-ca 1
1.050
180.000
2.000 same as X -c2-os-X
cd-cc-ca-ca 1
2.550
180.000
2.000 same as X -c2-ca-X
cc-cd-os-ca 1
1.050
180.000
2.000 same as X -c2-os-X
ca-ca-cc-ca 1
2.550
180.000
2.000 same as X -c2-ca-X
IMPROPER
c -cd-cc-i
1.1
180.0
2.0 Using default
value
cc-cd-cd-ha
1.1
180.0
2.0 Using default
value
cc-cd-cd-cd
1.1
180.0
2.0 Using default
value
cc-cd-cd-os
1.1
180.0
2.0 Using default
value
ca-ca-cc-cd
1.1
180.0
2.0 Using default
value
ca-ca-ca-os
1.1
180.0
2.0 Using default
value
ca-ca-ca-cc
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)
ca-ca-ca-oh
1.1
180.0
2.0 Using default
value
cc-cc-c -o
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-o -c -oh
10.5
180.0
2.0 General
improper torsional angle (2 general atom types)
NONBON
##################################################################
>>To be sure the COOH group is the problem, in your minimization .out
>>file, see which atom is reported for gradient max (GMAX).
NSTEP
ENERGY
RMS
GMAX
NAME NUMBER
100
-5.5260E+03 8.3251E+03
5.8941E+05
O4 1454
BOND =
129.1156 ANGLE =
1460.1636 DIHED
= 729.9489
VDWAALS = -2233.1513
EEL =
131.4737 HBOND
= 0.0000
1-4 VDW = 373.4535 1-4 EEL
= -6116.9878 RESTRAINT
= 0.0000
NSTEP
ENERGY
RMS
GMAX
NAME NUMBER
150
-5.4068E+07 2.8399E+11
1.6160E+13
H4 1456
BOND =
127.7585 ANGLE =
1459.8293 DIHED
= 728.7389
VDWAALS = -2233.1303
EEL =
131.5763 HBOND
= 0.0000
1-4 VDW = 373.4517 1-4 EEL =
************* RESTRAINT
= 0.0000
Atom correspond to either H(H4) or O(O5) of OH or O(O4) of C=O.
thanks and regards;
JIomm
_______________________________________________
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- Previous message: Thomas Cheatham: "Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial"
- In reply to: Bill Ross: "Re: [AMBER] COOH group troubling"
- Next in thread: Bill Ross: "Re: [AMBER] COOH group troubling"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
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