AMBER Archive (2009)
Subject: Re: [AMBER] PQR file - HELP PLEASE

From: s. Bill (s_bill36_at_yahoo.co.uk)
Date: Tue Dec 22 2009 - 15:27:48 CST

Previous message: davide branduardi: "[AMBER] pupil and amber"
In reply to: Jason Swails: "Re: [AMBER] PQR file - HELP PLEASE"
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Dear Dr. Jason
I am trying to calculate the binding energy of some ligands with a protein. In AMBER 10 manual, in page 223, it says:
# RADIOPT - option to set up radii and charges for PB calculation:
# 0: uses the radii from prmtop files
# 2: reads in PQR files with radii/charges information from
# lig.pqr, rec.pqr and com.pqr PQR files

In page 224, it says:
PQR files
With RADIOPT=2 three PQR files are required: lig.pqr, rec.pqr and com.pqr with charge/radius
information for the ligand, receptor and complex, respectively. This is the recommended
option to get better estimates of solvation energies.

So, I need to generate PQR files for my ligand, receptor and Complex. The main reason to generate these files is to avoid implementing the Zinc and calcuim ions radii in m_pbsa_calceneent.pm file, in addition, amber recommends that we should generate PQR files (regarding to comment in page 224).

Now, I am really confused, and I hope to find a clear answer for my questions:

***
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

* I generated PQR file for the same protien using pdb2pqr program and I got that:
ATOM 1 N PHE 1 -4.410 16.750 -3.770 0.1737 1.8240
ATOM 2 H PHE 1 -5.370 17.020 -3.680 0.1921 0.6000
ATOM 3 H2 PHE 1 -4.250 16.230 -4.630 0.1921 0.6000
ATOM 4 CA PHE 1 -3.940 15.790 -2.780 0.0733 1.9080
ATOM 5 HA PHE 1 -4.490 14.870 -2.990 0.1041 1.1000
ATOM 6 CB PHE 1 -2.370 15.430 -2.880 0.0330 1.9080
ATOM 7 HB2 PHE 1 -2.210 14.600 -2.200 0.0104 1.4870
ATOM 8 HB3 PHE 1 -2.280 15.060 -3.900 0.0104 1.4870
ATOM 9 CG PHE 1 -1.250 16.460 -2.560 0.0031 1.9080
ATOM 10 CD1 PHE 1 -1.150 16.760 -1.170 -0.1392 1.9080
ATOM 11 HD1 PHE 1 -1.710 16.210 -0.430 0.1374 1.4590
ATOM 12 CE1 PHE 1 -0.310 17.810 -0.780 -0.1602 1.9080
ATOM 13 HE1 PHE 1 -0.200 18.050 0.270 0.1433 1.4590
ATOM 14 CZ PHE 1 0.450 18.560 -1.700 -0.1208 1.9080
ATOM 15 HZ PHE 1 1.050 19.390 -1.340 0.1329 1.4590
ATOM 16 CE2 PHE 1 0.310 18.280 -3.090 -0.1603 1.9080
ATOM 17 HE2 PHE 1 0.710 18.860 -3.910 0.1433 1.4590
ATOM 18 CD2 PHE 1 -0.590 17.220 -3.510 -0.1391 1.9080
ATOM 19 HD2 PHE 1 -0.880 17.150 -4.550 0.1374 1.4590
ATOM 20 C PHE 1 -4.310 16.250 -1.370 0.6123 1.9080
ATOM 21 O PHE 1 -4.550 17.460 -1.150 -0.5713 1.6612
ATOM 22 H3 PHE 1 -3.926 17.627 -3.777 0.1921 0.6000

If we combared the ion radius generated using AMBER and that one generated using PDB2PQR program
we will find in AMBER carbon, for example, has a radius of 3.1 A while in PDB2PQR carbon has a radius of 1.9080 A
Why there is a differance?
Thanks for your help
S. Bill

--- On Tue, 22/12/09, Jason Swails <jason.swails_at_gmail.com> wrote:

From: Jason Swails <jason.swails_at_gmail.com>
Subject: Re: [AMBER] PQR file - HELP PLEASE
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Tuesday, 22 December, 2009, 17:21

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
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

-- --------------------------------------- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032

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Previous message: davide branduardi: "[AMBER] pupil and amber"
In reply to: Jason Swails: "Re: [AMBER] PQR file - HELP PLEASE"
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AMBER Archive (2009)Subject: Re: [AMBER] PQR file - HELP PLEASE

AMBER Archive (2009)
Subject: Re: [AMBER] PQR file - HELP PLEASE