AMBER Archive (2009)

Subject: Re: [AMBER] PQR files

From: Jason Swails (jason.swails_at_gmail.com)
Date: Fri Dec 25 2009 - 10:57:51 CST

Hello,

On Fri, Dec 25, 2009 at 9:38 AM, s. Bill <s_bill36_at_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

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