Dear Dr. Jason
Thanks again for your interest. Me too believe that, AMBER adds 1.4 A as shell around each radius. but why? and in this case should I take the PQR radius (generated by PDB2PQR) and add 1.4 to each radius value?
Also, where can I go back and read?
Thanks again for your interest.
Sincerely;
M. Ibrahim
--- On Fri, 25/12/09, Jason Swails <jason.swails.gmail.com> wrote:
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] PQR files
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Friday, 25 December, 2009, 16:57
Hello,
On Fri, Dec 25, 2009 at 9:38 AM, s. Bill <s_bill36.yahoo.co.uk> wrote:
> Dear AMBER
>
> 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 combpred 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?
>
I believe the amber radii have added a 1.4 Angstrom probe radius to
the atomic radii. Thus, the number you should be comparing to 1.9080
from PDB2PQR is actually 1.7, which is much closer. Someone else can
correct me if I'm wrong, but glancing at the code has led me to that
conclusion. It appears as though 1.7 Angstrom radius is given to C1,
C2, and C3; all other carbon atom types have a 2.2 Angstrom radius.
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Dec 25 2009 - 10:30:02 PST
