AMBER Archive (2009)

Subject: [AMBER] PQR files

From: s. Bill (s_bill36_at_yahoo.co.uk)
Date: Fri Dec 25 2009 - 08:38:36 CST

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?

Thanks for your help

S. Bill

      
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