Hi everyone,
This is a repost from GitHUB, in case someone has an idea around here (
https://github.com/ParmEd/ParmEd/issues/740#issuecomment-240732432). I'm
trying to assemble a system with a membrane protein that has a Cu+1 ion
interacting with it. I found out about the 12-6-4 implementation on AMBER
and wanted to try it. First, the copper +1 ion polarizability seems to be
missing from the lj_1264_pol.dat file. Also there was no info about
polarizabilities for lipid atoms. Considering that there are already a lot
of assumptions in the polarizability file, I included the missing values
comparing them to the values already present in the file, and calculated
the Cu+ polarizability with GAUSSIAN. Is this a correct approach or I'm
just plain wrong? Here are the values I included.
Cu+ 0.866 Caculated from B3LYP/6-311++G(2d,2p) level of theory
CU1 0.866 Caculated from B3LYP/6-311++G(2d,2p) level of theory
hL 0.387 Referenced or adopted from Miller JACS,112,8533(1990)
hB 0.387 Referenced or adopted from Miller JACS,112,8533(1990)
cC 1.352 Referenced or adopted from Miller JACS,112,8533(1990)
oC 0.569 Referenced or adopted from Miller JACS,112,8533(1990)
oS 0.637 Referenced or adopted from Miller JACS,112,8533(1990)
pA 1.538 Referenced or adopted from Miller JACS,112,8533(1990)
The cD atom doesn't seem to be missing, since parmed handles the file just
fine. Additionally, when I print the coefficient values, the C column
doesn't appear, but in the topology file the 1264 parameters are present.
Just for testing I tried a short MD sim, but even though it runs, it seems
unstable, which might be expected, since the changes I did.....
Here is the parmed output just in case. Any help would be great!
Adding Lennard-Jones C-coefficient for 12-6-4 potential.
Polarizabilities read from [Cu_membrane_LJ1264.pol]. Using default C4
parameters for water model [TIP3P].
***********************************************************
The selected metal ion is Cu
The biggest ATOM_TYPE_INDEX = 25
The selected +2 metal ion has the ATOM_TYPE_INDEX = 15
***********************************************************
Here are the atom types which have been added C4 term:
ATOM_TYPE_INDEX = 1 ; AMBER_ATOM_TYPE= N3 ; Polarizability= 1.09
ATOM_TYPE_INDEX = 2 ; AMBER_ATOM_TYPE= H ; Polarizability= 0.387
ATOM_TYPE_INDEX = 3 ; AMBER_ATOM_TYPE= CX ; Polarizability= 1.061
ATOM_TYPE_INDEX = 4 ; AMBER_ATOM_TYPE= HP ; Polarizability= 0.387
ATOM_TYPE_INDEX = 5 ; AMBER_ATOM_TYPE= HC ; Polarizability= 0.387
ATOM_TYPE_INDEX = 6 ; AMBER_ATOM_TYPE= H1 ; Polarizability= 0.387
ATOM_TYPE_INDEX = 7 ; AMBER_ATOM_TYPE= S ; Polarizability= 3.0
ATOM_TYPE_INDEX = 8 ; AMBER_ATOM_TYPE= C ; Polarizability= 1.352
ATOM_TYPE_INDEX = 9 ; AMBER_ATOM_TYPE= O ; Polarizability= 0.569
ATOM_TYPE_INDEX = 10 ; AMBER_ATOM_TYPE= H4 ; Polarizability= 0.387
ATOM_TYPE_INDEX = 11 ; AMBER_ATOM_TYPE= HA ; Polarizability= 0.387
ATOM_TYPE_INDEX = 12 ; AMBER_ATOM_TYPE= OH ; Polarizability= 0.637
ATOM_TYPE_INDEX = 13 ; AMBER_ATOM_TYPE= HO ; Polarizability= 0.0
ATOM_TYPE_INDEX = 14 ; AMBER_ATOM_TYPE= H5 ; Polarizability= 0.387
ATOM_TYPE_INDEX = 15 ; AMBER_ATOM_TYPE= Cu+ ; Polarizability= 0.866
ATOM_TYPE_INDEX = 16 ; AMBER_ATOM_TYPE= hL ; Polarizability= 0.387
ATOM_TYPE_INDEX = 17 ; AMBER_ATOM_TYPE= hB ; Polarizability= 0.387
ATOM_TYPE_INDEX = 18 ; AMBER_ATOM_TYPE= cC ; Polarizability= 1.352
ATOM_TYPE_INDEX = 19 ; AMBER_ATOM_TYPE= oC ; Polarizability= 0.569
ATOM_TYPE_INDEX = 20 ; AMBER_ATOM_TYPE= oS ; Polarizability= 0.637
ATOM_TYPE_INDEX = 21 ; AMBER_ATOM_TYPE= pA ; Polarizability= 1.538
ATOM_TYPE_INDEX = 22 ; AMBER_ATOM_TYPE= K+ ; Polarizability= 1.0571
ATOM_TYPE_INDEX = 23 ; AMBER_ATOM_TYPE= Cl- ; Polarizability= 3.235
ATOM_TYPE_INDEX = 24 ; AMBER_ATOM_TYPE= OW ; Polarizability= 1.444
ATOM_TYPE_INDEX = 25 ; AMBER_ATOM_TYPE= HW ; Polarizability= 0.0
***********************************************************
Atom Type 1 Atom Type
2 A coefficient B coefficient R i,j Eps i,j
------------------------------------------------------------------------------------------------------------------------------
N,N2,N3,NA,NB,nA [1] Cu+
[15] 9857.851660 24.929511 3.041000 0.015761
H,HS,hN [2] Cu+
[15] 6.202542 0.344723 1.817000 0.004790
2C,3C,C8,CT,CX,cA,cD [3] Cu+
[15] 10966.541800 23.550469 3.125000 0.012644
HP,hX [4] Cu+
[15] 114.662923 1.482166 2.317000 0.004790
HC [5] Cu+
[15] 731.797379 3.744387 2.704000 0.004790
H1,hE [6] Cu+
[15] 465.588625 2.986665 2.604000 0.004790
S,SH [7] Cu+
[15] 23482.455700 42.370847 3.217000 0.019113
C,C*,CA,CB,CC,CN,CO,CR,CV,CW,cB [8] Cu+
[15] 9723.223350 20.880463 3.125000 0.011210
O,O2 [9] Cu+
[15] 5661.376650 19.917106 2.878200 0.017517
H4 [10] Cu+
[15] 503.434607 3.070469 2.626000 0.004682
HA [11] Cu+
[15] 631.305706 3.438374 2.676000 0.004682
OH [12] Cu+
[15] 7252.790640 22.554042 2.938000 0.017534
HO [13] Cu+
[15] 0.000000 0.000000 0.000000 0.000000
H5 [14] Cu+
[15] 399.720765 2.735971 2.576000 0.004682
Cu+ [15] Cu+
[15] 63.178373 0.607680 2.434000 0.001461
Cu+ [15] hL
[16] 517.775182 2.813721 2.677000 0.003823
Cu+ [15] hB
[17] 162.532266 1.441965 2.467000 0.003198
Cu+ [15] cC
[18] 8772.230930 18.838223 3.125000 0.010114
Cu+ [15] oC,oP
[19] 4411.203660 15.886234 2.867000 0.014303
Cu+ [15] oS,oT
[20] 4083.981010 14.707795 2.867000 0.013242
Cu+ [15] pA
[21] 30326.440000 45.538487 3.317000 0.017095
Cu+ [15] K+
[22] 7794.998890 22.486623 2.975000 0.016217
Cu+ [15] Cl-
[23] 58602.860600 80.443343 3.367000 0.027606
Cu+ [15] OW
[24] 7466.865720 21.097959 2.985300 0.014903
Cu+ [15] HW
[25] 0.000000 0.000000 0.000000 0.000000
--
Stephan Schott V.
Bioquímico / Licenciado en Bioquímica
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Received on Tue Aug 23 2016 - 08:00:03 PDT
