Dear Amber community,
I am in the process of building amino-acid variants for simulations. Our
interest lies in protonated/deprotonated versions of existing amino acids
for "gas-phase" calculations. After some testing on an arginine residue, we
decided that calculations will be run at a B3LYP/6-31G* level. In any other
respect I am trying to follow the J. Comp. Chem. 1995 paper as well as
possible.
The first problem that we have encountered was building the starting
geometries stated in table II, p. 1362 in the aforementioned paper. It would
really help if the coordinated for these geometries were available.
Furthermore, how significant is it to start the calculations from such a
geometry? Especially for the 'idealised' alpha-helical torsions (-60, -40),
the conformation of backbone atoms is not retained after optimisation. The
C5 geometry seems to 'survive' more frequently.
Now, my main question is about the multi-molecular RESP fitting method. I
have followed all instructions available to extract the ESP data for two
conformations of the residue (it is a C-terminal amidated Alanine) from the
Gaussian output files, catenated the two, then generated resp input files
for the fit. The input for the first fitting step looks like this:
Resp charges for organic molecule
&cntrl
nmol = 2,
ihfree = 1,
ioutopt = 1,
&end
130.0
Resp charges for organic molecule
0 19
1 0
6 0
1 0
1 0
6 0
8 0
7 0
1 0
6 0
1 0
6 0
8 0
6 0
1 0
1 0
1 0
7 0
1 0
1 18
130.0
Resp charges for organic molecule
0 19
1 0
6 0
1 0
1 0
6 0
8 0
7 0
1 0
6 0
1 0
6 0
8 0
6 0
1 0
1 0
1 0
7 0
1 0
1 18
6 0
1 1 1 2 1 3 1 4 1 5 1 6
2
1 1 2 1
2
1 2 2 2
2
1 3 2 3
2
1 4 2 4
2
1 5 2 5
2
1 6 2 6
2
1 7 2 7
2
1 8 2 8
2
1 9 2 9
2
1 10 2 10
2
1 11 2 11
2
1 12 2 12
2
1 13 2 13
2
1 14 2 14
2
1 15 2 15
2
1 16 2 16
2
1 17 2 17
2
1 18 2 18
2
1 19 2 19
With the constraints I'm trying to achieve the following:
- Make all 'identical' atoms from the two conformations equivalent
- Impose a net charge of zero to the capping group (an acetyl moiety - first
six atoms)
Unfortunately though, with the current setup I get the following output
file:
-----------------------------------------------
Restrained ESP Fit 2.3 Amber 4.1
-----------------------------------------------
Resp charges for organic molecule
-----------------------------------------------
inopt = 0 ioutopt = 1
nmol = 2 iqopt = 0
ihfree = 1 irstrnt = 1
iunits = 0 qwt = 0.00050000
%RESP-I-MULT_MOL, multiple-molecule run of 2 molecules
Reading input for molecule 1 weight: 130.000
Resp charges for organic molecule
Total charge (ich): 0
Number of centers: 19
1 1 0
2 6 0
3 1 0
4 1 0
5 6 0
6 8 0
7 7 0
8 1 0
9 6 0
10 1 0
11 6 0
12 8 0
13 6 0
14 1 0
15 1 0
16 1 0
17 7 0
18 1 0
19 1 18
Reading input for molecule 2 weight: 130.000
Resp charges for organic molecule
Total charge (ich): 0
Number of centers: 19
20 1 0
21 6 0
22 1 0
23 1 0
24 6 0
25 8 0
26 7 0
27 1 0
28 6 0
29 1 0
30 6 0
31 8 0
32 6 0
33 1 0
34 1 0
35 1 0
36 7 0
37 1 0
38 1 18
--------------------------------
reading mult_mol constraint info
--------------------------------
1 1 1 2 1 3 1 4 1 5 1 6
1 1 2 1
1 2 2 2
1 3 2 3
1 4 2 4
1 5 2 5
1 6 2 6
1 7 2 7
1 8 2 8
1 9 2 9
1 10 2 10
1 11 2 11
1 12 2 12
1 13 2 13
1 14 2 14
1 15 2 15
1 16 2 16
1 17 2 17
1 18 2 18
1 19 2 19
--------------------
Atom Ivary
--------------------
1 0
6 1
1 1
1 1
6 1
8 1
7 0
1 0
6 0
1 0
6 0
8 0
6 0
1 0
1 0
1 0
7 0
1 0
1 18
1 1
6 1
1 1
1 1
6 1
8 1
7 7
1 8
6 9
1 10
6 11
8 12
6 13
1 14
1 15
1 16
7 17
1 18
1 18
----------------------------------------------------------------------------
Total number of atoms = 38
Weight factor on initial charge restraints= 0.000500
There are 2 charge constraints
Reading esp"s for molecule 1
total number of atoms = 19
total number of esp points = 5800
center X Y Z
1 0.5244048E+01 -0.1457098E+01 -0.3127389E+01
2 0.5739154E+01 -0.7333327E+00 -0.1252781E+01
3 0.6891891E+01 -0.2131726E+01 -0.2625642E+00
4 0.6899441E+01 0.9674244E+00 -0.1487107E+01
5 0.3460143E+01 -0.8705212E-01 0.3761632E+00
6 0.3643445E+01 0.2927828E+00 0.2647614E+01
7 0.1184913E+01 0.1687525E-01 -0.8880635E+00
8 0.1222708E+01 -0.4359598E-01 -0.2798576E+01
9 -0.1099770E+01 0.1024093E+01 0.2911255E+00
10 -0.6254483E+00 0.1184722E+01 0.2301794E+01
11 -0.3359876E+01 -0.8108380E+00 0.1229399E+00
12 -0.5531173E+01 -0.7007104E-01 0.3780529E+00
13 -0.1812204E+01 0.3633803E+01 -0.7387752E+00
14 -0.3565871E+01 0.4272525E+01 0.1399474E+00
15 -0.3060959E+00 0.4994410E+01 -0.3381532E+00
16 -0.2120229E+01 0.3569551E+01 -0.2787238E+01
17 -0.2757046E+01 -0.3282598E+01 -0.3022484E+00
18 -0.9447968E+00 -0.3866517E+01 -0.2002032E+00
19 -0.4153550E+01 -0.4571395E+01 -0.1057169E+00
Reading esp"s for molecule 2
total number of atoms = 19
total number of esp points = 5736
center X Y Z
1 -0.4955020E+01 -0.3620564E+01 0.1067614E+01
2 -0.5644746E+01 -0.1866889E+01 0.2134578E+00
3 -0.6614181E+01 -0.2314741E+01 -0.1557216E+01
4 -0.7037462E+01 -0.1005155E+01 0.1477685E+01
5 -0.3567910E+01 0.4737354E-01 -0.3232244E+00
6 -0.4013856E+01 0.2116631E+01 -0.1277536E+01
7 -0.1188755E+01 -0.6802031E+00 0.3362900E+00
8 -0.7938266E+00 -0.2445213E+01 0.9674584E+00
9 0.9995687E+00 0.8787887E+00 -0.1909436E+00
10 0.7558073E+00 0.1729169E+01 -0.2067442E+01
11 0.3308789E+01 -0.8805783E+00 -0.2041717E+00
12 0.3218052E+01 -0.3031085E+01 0.6537639E+00
13 0.1311404E+01 0.3025514E+01 0.1755474E+01
14 0.2929026E+01 0.4233026E+01 0.1300050E+01
15 -0.3987813E+00 0.4182050E+01 0.1740356E+01
16 0.1587294E+01 0.2246943E+01 0.3652759E+01
17 0.5463092E+01 0.1360640E+00 -0.1171711E+01
18 0.5499021E+01 0.1844376E+01 -0.2014529E+01
19 0.7031549E+01 -0.9505511E+00 -0.1232183E+01
Initial ssvpot = 74200.412
Number of unique UNfrozen centers= 13
Non-linear optimization requested.
qchnge = 0.8392109792E-01
qchnge = 0.5704251783E-07
qchnge = 0.3061276458E-12
Convergence in 2 iterations
Resp charges for organic molecule
Point Charges Before & After Optimization
no. At.no. q(init) q(opt) ivary d(rstr)/dq
1 1 0.000000 0.001696 0 0.000000
2 6 0.000000 0.001696 1 0.004999
3 1 0.000000 0.001696 1 0.000000
4 1 0.000000 0.001696 1 0.000000
5 6 0.000000 0.001696 1 0.004999
6 8 0.000000 0.001696 1 0.004999
7 7 0.000000 -0.536747 0 0.000916
8 1 0.000000 0.507795 0 0.000000
9 6 0.000000 -0.297137 0 0.001595
10 1 0.000000 -0.036016 0 0.000000
11 6 0.000000 1.199541 0 0.000415
12 8 0.000000 -0.669359 0 0.000739
13 6 0.000000 0.245507 0 0.001886
14 1 0.000000 0.000739 0 0.000000
15 1 0.000000 -0.049329 0 0.000000
16 1 0.000000 -0.059168 0 0.000000
17 7 0.000000 -1.386707 0 0.000360
18 1 0.000000 0.535351 0 0.000000
19 1 0.000000 0.535351 18 0.000000
20 1 0.000000 0.001696 1 0.000000
21 6 0.000000 0.001696 1 0.004999
22 1 0.000000 0.001696 1 0.000000
23 1 0.000000 0.001696 1 0.000000
24 6 0.000000 0.001696 1 0.004999
25 8 0.000000 0.001696 1 0.004999
26 7 0.000000 -0.536747 7 0.000916
27 1 0.000000 0.507795 8 0.000000
28 6 0.000000 -0.297137 9 0.001595
29 1 0.000000 -0.036016 10 0.000000
30 6 0.000000 1.199541 11 0.000415
31 8 0.000000 -0.669359 12 0.000739
32 6 0.000000 0.245507 13 0.001886
33 1 0.000000 0.000739 14 0.000000
34 1 0.000000 -0.049329 15 0.000000
35 1 0.000000 -0.059168 16 0.000000
36 7 0.000000 -1.386707 17 0.000360
37 1 0.000000 0.535351 18 0.000000
38 1 0.000000 0.535351 18 0.000000
Sum over the calculated charges: 0.000
Statistics of the fitting:
The initial sum of squares (ssvpot) 74200.412
The residual sum of squares (chipot) 74197.016
The std err of estimate (sqrt(chipot/N)) 3.59657
ESP relative RMS (SQRT(chipot/ssvpot)) 0.99998
Obviously, the charge constraint for the first 6 atoms does not set the net
charge to zero, but 'forces' every atom to have a charge of (almost) zero.
This makes the fit a bit "irregular" (attributing e.g. unusually high
charges to particular atoms). Is there a way to correct this behaviour? I
have tried different 'spacing' versions of my input file but this is the
best result I've got so far, which is obviously not good enough. I will be
very grateful if anyone could help me on this matter!
I will attached the esp file for your reference. Any advice will be greatly
appreciated.
Jason
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- application/octet-stream attachment: ACM.esp
Received on Wed Apr 12 2006 - 06:07:11 PDT