S. Bill,
What exactly are you trying to run MM-PBSA for that you need a PQR
file? We have just released a new MMPBSA script that bypasses the
need for a PQR file (all of the charges and radii are in the prmtop
anyway) (it doesn't use delphi if that's what you're trying to use,
but it does use the internal pb solver or APBS).
You can access the new script at
www.ambermd.org/tutorials/advanced/tutorial3/py_script along with
instructions on how to use it.
Good luck!
Jason
On Tue, Dec 22, 2009 at 7:57 AM, s. Bill <s_bill36.yahoo.co.uk> wrote:
> Dear AMBER
> I run MM-PBSA on one protien containing Zn ion. During the PQR file generation the process stop, I do know becuase there is no radius of Zn ion defined in PQR.
> I want just to ask about the PQR file:
> the second last and last column are charge and radius, respectivly, aren't they?
> ok, why charge here in my file is zero?
> and what kind of radius is this one, in which carbon is 3.1 A?
>
> ATOM 1 N PHE 1 -4.410 16.750 -3.770 0.00 2.95
> ATOM 2 H1 PHE 1 -5.370 17.020 -3.680 0.00 2.60
> ATOM 3 H2 PHE 1 -4.250 16.230 -4.630 0.00 2.60
> ATOM 4 H2 PHE 1 -3.760 17.520 -3.830 0.00 2.60
> ATOM 5 CA PHE 1 -3.940 15.790 -2.780 0.00 3.10
> ATOM 6 HA PHE 1 -4.490 14.870 -2.990 0.00 2.60
> ATOM 7 CB PHE 1 -2.370 15.430 -2.880 0.00 3.10
> ATOM 8 HB2 PHE 1 -2.210 14.600 -2.200 0.00 2.60
> ATOM 9 HB3 PHE 1 -2.280 15.060 -3.900 0.00 2.60
> ATOM 10 CG PHE 1 -1.250 16.460 -2.560 0.00 3.10
> ATOM 11 CD1 PHE 1 -1.150 16.760 -1.170 0.00 3.10
> ATOM 12 HD1 PHE 1 -1.710 16.210 -0.430 0.00 2.60
> ATOM 13 CE1 PHE 1 -0.310 17.810 -0.780 0.00 3.10
> ATOM 14 HE1 PHE 1 -0.200 18.050 0.270 0.00 2.60
> ATOM 15 CZ PHE 1 0.450 18.560 -1.700 0.00 3.10
> ATOM 16 HZ PHE 1 1.050 19.390 -1.340 0.00 2.60
> ATOM 17 CE2 PHE 1 0.310 18.280 -3.090 0.00 3.10
> ATOM 18 HE2 PHE 1 0.710 18.860 -3.910 0.00 2.60
> ATOM 19 CD2 PHE 1 -0.590 17.220 -3.510 0.00 3.10
> ATOM 20 HD2 PHE 1 -0.880 17.150 -4.550 0.00 2.60
> ATOM 21 C PHE 1 -4.310 16.250 -1.370 0.00 3.10
> ATOM 22 O PHE 1 -4.550 17.460 -1.150 0.00 2.90
>
> Help needed.
> Thanks in advance
> S. Bill
>
>
>
>
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Dec 22 2009 - 09:30:03 PST
