From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jan 20 2006 - 09:14:56 CST

Hi Lavina,
Could you be more specific about what the first error is? I don't see
anything except for the missing parameters.

As far as the second error, as a general rule to run simulations using
the charmm forcefield you need topologies and parameters for all of the
molecules you're going to use. The standard topology and paramter files
contain all of the amino acids, DNA/RNA and some common lipids, but
topology files for other ligands must be obtained from other sources.
Parameterizing unknown molecules on your own is always an option but
involves some QM simulations; Paratool is a VMD plugin under development
to deal with this, but requires that you have the /ab initio/ QM program
Gaussian. If you click on the parameterize button in autopsf's window,
it will lead you to paratool. Since biotin is a fairly common molecule,
it is likely that someone else has developed parameters for it, so you
may have some success searching for biotin charmm parameters on the
internet. You may also wish to contact the lead author of the biotin
paper that you mentioned earlier. Once you have the topology and
parameter files you need, you can load the topology file for biotin into
autopsf and then run it normally.

Best,
Peter

Lin wrote:

>hi all, i have problem generating the psf of biotin.
>it gives me two errors,
>1)problem with input file structure
>2)it says there are some missing parameters in the file,
>and it asks me to parameterize the molecule.
>
>Does anybody have any idea what is the problem?
>
>Thank you very much!
>
>Regards,
>Lavina
>
>
>
>
>
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>------------------------------------------------------------------------
>
>CRYST1 80.150 80.150 85.280 90.00 90.00 90.00 P 1 1
>ATOM 1 C1 BTN X 401 50.145 -1.395 42.903 1.00 46.67 1AVD
>ATOM 2 C10 BTN X 401 51.508 -1.294 42.213 1.00 4.00 1AVD
>ATOM 3 C9 BTN X 401 51.407 -0.358 40.959 1.00 21.78 1AVD
>ATOM 4 C8 BTN X 401 52.619 0.527 40.667 1.00 23.04 1AVD
>ATOM 5 C7 BTN X 401 52.393 1.684 39.649 1.00 45.96 1AVD
>ATOM 6 C2 BTN X 401 51.148 1.712 38.694 1.00 12.11 1AVD
>ATOM 7 C6 BTN X 401 50.132 2.153 36.321 1.00 11.45 1AVD
>ATOM 8 C4 BTN X 401 51.070 3.188 38.298 1.00 12.68 1AVD
>ATOM 9 C5 BTN X 401 50.454 3.488 36.950 1.00 41.53 1AVD
>ATOM 10 C3 BTN X 401 52.667 4.335 36.965 1.00 35.90 1AVD
>ATOM 11 O1 BTN X 401 49.691 -0.242 43.365 1.00 6.52 1AVD
>ATOM 12 O2 BTN X 401 49.424 -2.377 42.860 1.00 24.49 1AVD
>ATOM 13 O3 BTN X 401 53.731 4.889 36.649 1.00 20.37 1AVD
>ATOM 14 N1 BTN X 401 51.518 4.264 36.273 1.00 11.57 1AVD
>ATOM 15 N2 BTN X 401 52.465 3.638 38.102 1.00 20.86 1AVD
>ATOM 16 S1 BTN X 401 51.478 1.102 36.976 1.00 29.73 1AVD
>END
>
>