AMBER Archive (2009)

Subject: Re: [AMBER] PQR file - HELP PLEASE

From: Jason Swails (jason.swails_at_gmail.com)
Date: Tue Dec 22 2009 - 11:21:41 CST

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_at_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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