Dear Iqbal, Muhammad Sajid,
Concerning PEG the problem is the length of PEG ... and PEGs of
different lengths. So I would like to suggest you to use the building
block approach implemented in R.E.D. Server Dev./PyRED...
See also the F-84 project in REDDB
http://q4md-forcefieldtools.org/REDDB/projects/F-84/
In your case you can split PEG into three molecular fragments:
C-terminal, Central and OH-terminal.
Me-OCH2CH2-OH
you set an intra-mcc
(intra-mcc1 or intra-mcc2 between the Me and OH groups; intra-mcc2
might be more suitable for an exact PEG molecule)
PyRED will generate there fragments:
Me-OCH2CH2
OCH2CH2
OCH2CH2-OH
You will be able to generate PEG of different lengths, n:
Me-OCH2CH2-(OCH2CH2)n-OCH2CH2-OH
The whole molecule approach as implemented in Antechamber is limited
because you will have to derive charges for the PEG molecules of
different lengths...
regards, Franncois
> I have tried leaprc.gcff force field for PEG to generate topology and
> coordinate files but it gives me error that first three atoms are not
> defined. could any one please help me how to fix it ?
>
> Error message;
>
> FATAL: Atom .R< 1>.A<H 1> does not have a type.
> FATAL: Atom .R< 1>.A<O 2> does not have a type.
> FATAL: Atom .R< 1>.A<C 3> does not have a type.
>
> coordinates from pdb file
>
> ATOM 1 H 1 16.667 16.667 16.667 0.00 1.00
> H 0.0000
> ATOM 2 O 1 16.685 16.550 17.594 3.07 1.00
> O 0.0000
> ATOM 3 C 1 15.466 15.899 17.883 3.40 1.00
> C 0.0000
> ATOM 4 H 1 15.593 15.384 18.868 2.47 1.00
> H 0.0000
> ATOM 5 H 1 15.213 15.177 17.064 2.47 1.00
> H 0.0000
> ATOM 6 C 1 14.522 17.057 17.896 3.40 1.00
> C 0.0000
> ATOM 7 H 1 14.829 17.769 18.628 2.47 1.00
> H 0.0000
> ATOM 8 H 1 13.599 16.718 18.228 2.47 1.00
> H 0.0000
> ATOM 9 O 1 14.425 17.768 16.675 3.00 1.00
> O 0.0000
> ATOM 10 C 1 13.351 18.612 16.851 3.40 1.00
> C 0.0000
> ATOM 11 H 1 13.467 19.123 17.824 2.47 1.00
> H 0.0000
> ATOM 12 H 1 12.377 18.188 16.782 2.47 1.00
> H 0.0000
> ATOM 13 C 1 13.448 19.727 15.707 3.40 1.00
> C 0.0000
> ATOM 14 H 1 14.439 19.900 15.300 2.47 1.00
> H 0.0000
> ATOM 15 H 1 13.021 20.619 16.216 2.47 1.00
> H 0.0000
> ATOM 16 O 1 12.471 19.455 14.734 3.00 1.00
> O 0.0000
> ATOM 17 C 1 12.169 20.621 14.075 3.40 1.00
> C 0.0000
> ATOM 18 H 1 13.112 21.068 13.685 2.47 1.00
> H 0.0000
> ATOM 19 H 1 11.711 21.371 14.715 2.47 1.00
> H 0.0000
> ATOM 20 C 1 11.164 20.415 12.973 3.40 1.00
> C 0.0000
> ATOM 21 H 1 10.714 21.405 12.769 2.47 1.00
> H 0.0000
> ATOM 22 H 1 10.412 19.703 13.312 2.47 1.00
> H 0.0000
> ATOM 23 O 1 11.896 19.896 11.798 3.00 1.00
> O 0.0000
> ATOM 24 C 1 11.054 19.825 10.616 3.40 1.00
> C 0.0000
> ATOM 25 H 1 10.483 20.763 10.463 2.47 1.00
> H 0.0000
> ATOM 26 H 1 10.268 19.055 10.895 2.47 1.00
> H 0.0000
> ATOM 27 C 1 11.808 19.372 9.368 3.40 1.00
> C 0.0000
> ATOM 28 H 1 12.374 20.176 8.953 2.47 1.00
> H 0.0000
> ATOM 29 H 1 11.021 19.025 8.694 2.47 1.00
> H 0.0000
> ATOM 30 O 1 12.645 18.290 9.625 3.00 1.00
> O 0.0000
> ATOM 31 C 1 13.223 17.954 8.398 3.40 1.00
> C 0.0000
> ATOM 32 H 1 12.497 17.812 7.602 2.47 1.00
> H 0.0000
> ATOM 33 H 1 13.929 18.694 7.965 2.47 1.00
> H 0.0000
> ATOM 34 C 1 13.924 16.578 8.498 3.40 1.00
> C 0.0000
> ATOM 35 H 1 14.294 16.228 7.506 2.47 1.00
> H 0.0000
> ATOM 36 H 1 13.411 15.776 8.975 2.47 1.00
> H 0.0000
> ATOM 37 O 1 15.217 16.737 9.214 3.00 1.00
> O 0.0000
> ATOM 38 C 1 15.914 15.527 9.338 3.40 1.00
> C 0.0000
> ATOM 39 H 1 16.042 15.010 8.362 2.47 1.00
> H 0.0000
> ATOM 40 H 1 15.344 14.861 10.008 2.47 1.00
> H 0.0000
> ATOM 41 C 1 17.327 15.739 9.961 3.40 1.00
> C 0.0000
> ATOM 42 H 1 18.009 15.110 9.518 2.47 1.00
> H 0.0000
> ATOM 43 H 1 17.737 16.731 9.766 2.47 1.00
> H 0.0000
> ATOM 44 O 1 17.312 15.595 11.343 3.00 1.00
> O 0.0000
> ATOM 45 C 1 16.430 16.534 11.911 3.40 1.00
> C 0.0000
> ATOM 46 H 1 16.672 17.534 11.637 2.47 1.00
> H 0.0000
> ATOM 47 H 1 15.349 16.409 11.677 2.47 1.00
> H 0.0000
> ATOM 48 C 1 16.580 16.545 13.480 3.40 1.00
> C 0.0000
> ATOM 49 H 1 15.888 17.285 13.823 2.47 1.00
> H 0.0000
> ATOM 50 H 1 17.579 16.881 13.750 2.47 1.00
> H 0.0000
> ATOM 51 O 1 16.337 15.205 13.885 3.00 1.00
> O 0.0000
> ATOM 52 C 1 17.494 14.425 13.850 3.40 1.00
> C 0.0000
> ATOM 53 H 1 17.557 13.998 12.853 2.47 1.00
> H 0.0000
> ATOM 54 H 1 18.431 14.934 14.127 2.47 1.00
> H 0.0000
> ATOM 55 C 1 17.439 13.209 14.742 3.40 1.00
> C 0.0000
> ATOM 56 H 1 18.213 12.490 14.459 2.47 1.00
> H 0.0000
> ATOM 57 H 1 16.500 12.697 14.464 2.47 1.00
> H 0.0000
> ATOM 58 O 1 17.509 13.431 16.163 3.00 1.00
> O 0.0000
> ATOM 59 C 1 18.729 14.027 16.565 3.40 1.00
> C 0.0000
> ATOM 60 H 1 19.475 13.392 16.249 2.47 1.00
> H 0.0000
> ATOM 61 H 1 18.902 14.997 16.162 2.47 1.00
> H 0.0000
> ATOM 62 C 1 18.758 14.067 18.126 3.40 1.00
> C 0.0000
> ATOM 63 H 1 18.340 13.134 18.551 2.47 1.00
> H 0.0000
> ATOM 64 H 1 18.217 14.851 18.605 2.47 1.00
> H 0.0000
> ATOM 65 O 1 20.109 14.117 18.541 3.07 1.00
> O 0.0000
> ATOM 66 H 1 20.028 14.134 19.538 0.00 1.00
> H 0.0000
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Received on Thu Jul 10 2014 - 03:00:03 PDT
