[gmx-users] Re: Organic Molecules
Michael Brunsteiner
mbx0009 at yahoo.com
Sat Sep 18 13:29:45 CEST 2004
PEO - you are talking about polyethylene oxide, are you ?
A while ago I made myself a topology for one of these,
its CH3-O-(CH2-CH2-O)_4-CH3.
I used OPLS parameters and ESPD charges, calculated
with DFT/LDA (DMol3), should be a fairly decent model ...
extension to longer (or shorter) chains is straightforward.
The rtp-entry and the corresponding PDB-file are included below.
You need to include it into your ffoplsaa.rtp file
then you can make the topology of an arbitrary number of
these, including solvent or any other molecules that
are covered by OPLS using pdb2gmx. (be careful to retain
the correct residue-name, atom names and sequence of atoms
for the PEO in your PDB file)
best wishes
Michael
; the rtp-entry ...
; ########################################################################
; C_10 O_5 H_22 (ethylene oxide)
[ eo5 ]
[ atoms ]
H03 opls_185 0.100 1
C02 opls_181 -0.240 2
H04 opls_185 0.100 3
H05 opls_185 0.100 4
O01 opls_180 -0.360 5
C03 opls_182 0.050 6
H06 opls_185 0.080 7
H07 opls_185 0.080 8
C04 opls_182 0.050 9
H08 opls_185 0.080 10
H09 opls_185 0.080 11
O02 opls_180 -0.360 12
C05 opls_182 0.050 13
H10 opls_185 0.080 14
H11 opls_185 0.080 15
C06 opls_182 0.050 16
H12 opls_185 0.080 17
H13 opls_185 0.080 18
O03 opls_180 -0.360 19
C07 opls_182 0.050 20
H14 opls_185 0.080 21
H15 opls_185 0.080 22
C08 opls_182 0.050 23
H16 opls_185 0.080 24
H17 opls_185 0.080 25
O04 opls_180 -0.360 26
C09 opls_182 0.050 27
H18 opls_185 0.080 28
H19 opls_185 0.080 29
C10 opls_182 0.050 30
H20 opls_185 0.080 31
H21 opls_185 0.080 32
O05 opls_180 -0.360 33
C01 opls_181 -0.240 34
H00 opls_185 0.100 35
H02 opls_185 0.100 36
H01 opls_185 0.100 37
[bonds]
H03 C02 ; 1.11169 100000.0
C02 H04 ; 1.10039 100000.0
C02 H05 ; 1.11262 100000.0
C02 O01 ; 1.39713 100000.0
O01 C03 ; 1.39735 100000.0
C03 H06 ; 1.11585 100000.0
C03 H07 ; 1.11347 100000.0
C03 C04 ; 1.50633 100000.0
C04 H08 ; 1.10428 100000.0
C04 H09 ; 1.11040 100000.0
C04 O02 ; 1.40563 100000.0
O02 C05 ; 1.40626 100000.0
C05 H10 ; 1.10664 100000.0
C05 H11 ; 1.11081 100000.0
C05 C06 ; 1.51118 100000.0
C06 H12 ; 1.10768 100000.0
C06 H13 ; 1.11049 100000.0
C06 O03 ; 1.40594 100000.0
O03 C07 ; 1.40462 100000.0
C07 H14 ; 1.10501 100000.0
C07 H15 ; 1.11125 100000.0
C07 C08 ; 1.50506 100000.0
C08 H16 ; 1.11274 100000.0
C08 H17 ; 1.11618 100000.0
C08 O04 ; 1.39897 100000.0
O04 C09 ; 1.40049 100000.0
C09 H18 ; 1.11236 100000.0
C09 H19 ; 1.11294 100000.0
C09 C10 ; 1.50052 100000.0
C10 H20 ; 1.11371 100000.0
C10 H21 ; 1.11414 100000.0
C10 O05 ; 1.39734 100000.0
O05 C01 ; 1.39753 100000.0
C01 H00 ; 1.11208 100000.0
C01 H02 ; 1.11275 100000.0
C01 H01 ; 1.10184 100000.0
; here starts the PDB file of one PEO_5
ATOM 1 C01 peo P 1 1.148 1.130 -0.736 0.00 0.00
ATOM 2 H01 peo P 1 0.966 1.000 0.239 0.00 0.00
ATOM 3 H02 peo P 1 2.118 1.269 -0.536 0.00 0.00
ATOM 4 H03 peo P 1 0.178 0.992 -0.936 0.00 0.00
ATOM 5 C02 peo P 1 0.987 2.112 -0.634 0.00 0.00
ATOM 6 H04 peo P 1 1.957 2.250 -0.435 0.00 0.00
ATOM 7 H05 peo P 1 0.017 1.973 -0.834 0.00 0.00
ATOM 8 O01 peo P 1 0.826 3.094 -0.533 0.00 0.00
ATOM 9 C03 peo P 1 0.665 4.075 -0.431 0.00 0.00
ATOM 10 H06 peo P 1 1.635 4.214 -0.231 0.00 0.00
ATOM 11 H07 peo P 1 -0.305 3.937 -0.631 0.00 0.00
ATOM 12 C04 peo P 1 0.504 5.057 -0.330 0.00 0.00
ATOM 13 H08 peo P 1 1.474 5.196 -0.130 0.00 0.00
ATOM 14 H09 peo P 1 -0.466 4.918 -0.530 0.00 0.00
ATOM 15 O02 peo P 1 0.343 6.039 -0.228 0.00 0.00
ATOM 16 C05 peo P 1 0.181 7.020 -0.127 0.00 0.00
ATOM 17 H10 peo P 1 1.151 7.159 0.073 0.00 0.00
ATOM 18 H11 peo P 1 -0.789 6.882 -0.327 0.00 0.00
ATOM 19 C06 peo P 1 0.020 8.002 -0.025 0.00 0.00
ATOM 20 H12 peo P 1 0.990 8.141 0.175 0.00 0.00
ATOM 21 H13 peo P 1 -0.950 7.864 -0.225 0.00 0.00
ATOM 22 O03 peo P 1 -0.141 8.984 0.076 0.00 0.00
ATOM 23 C07 peo P 1 -0.302 9.966 0.178 0.00 0.00
ATOM 24 H14 peo P 1 0.668 10.104 0.378 0.00 0.00
ATOM 25 H15 peo P 1 -1.272 9.827 -0.022 0.00 0.00
ATOM 26 C08 peo P 1 -0.463 10.947 0.279 0.00 0.00
ATOM 27 H16 peo P 1 0.507 11.086 0.479 0.00 0.00
ATOM 28 H17 peo P 1 -1.433 10.809 0.079 0.00 0.00
ATOM 29 O04 peo P 1 -0.624 11.929 0.381 0.00 0.00
ATOM 30 C09 peo P 1 -0.785 12.911 0.482 0.00 0.00
ATOM 31 H18 peo P 1 0.185 13.049 0.682 0.00 0.00
ATOM 32 H19 peo P 1 -1.755 12.772 0.283 0.00 0.00
ATOM 33 C10 peo P 1 -0.946 13.892 0.584 0.00 0.00
ATOM 34 H20 peo P 1 0.024 14.031 0.784 0.00 0.00
ATOM 35 H21 peo P 1 -1.916 13.754 0.384 0.00 0.00
ATOM 36 O05 peo P 1 -1.107 14.874 0.685 0.00 0.00
ATOM 37 H22 peo P 1 -1.289 14.743 1.660 0.00 0.00
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