[Bug] - Wrong format in I/O of site files

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jasalim
Posts: 1
Joined: Wed Dec 03, 2014 6:35 am

[Bug] - Wrong format in I/O of site files

Post by jasalim » Fri Jan 29, 2016 7:05 am

Hi,
I found a possible error during the input/output of site files. I will try to explain what I did and what happened.
First, I ran delphi with follow parameters file and it generates the output 2fsxA.chrg:

Code: Select all

!fort.10
perfil=80
scale=2.5
in(pdb,file="2fsxA.pdb")
in(siz,file="../data/parse3_red.siz")
in(crg,file="../data/parse3_newn_reduce.crg")
in(frc,frm=self)
out(frc,file="2fsxA.frc")
out(scrg,frm=PDB,file="2fsxA.chrg")
atompotdist=0.6
site(q,p,atpo)
indi=2.0
exdi=80.0
prbrad=1.4
ionrad=2.0
salt=0.0000
bndcon=4
linit=500
maxc=.0002
Then I used this file as input of another execution using the follow parameters file to generates the 2fsxA.pot]\b] file:

Code: Select all

!fort.10.1
perfil=80
scale=2.5
in(pdb,file="2fsxA.pdb")
in(siz,file="../data/parse3_red.siz")
in(crg,file="../data/parse3_newn_reduce.crg")
in(frc,file="2fsxA.chrg")
out(frc,file="2fsxA.pot")
site(x,p)
indi=2.0
exdi=80.0
prbrad=1.4
ionrad=2.0
salt=0.0000
bndcon=4
linit=500
maxc=.0002
During the second execution a have got lots of WARNING messages like this:

PAY ATTENSION, POINT OUT OF THE CUBE!!
VALUES: 84.0962 16108.5 -43.4514 GRID: 135
VALUE AT THIS POINT IS SET = 0.
[\b]
(with miss written ATTENSION, instead of ATTENTION)

Looking the warning message the atoms coordinates shows strange values like this above: 16108.5. Some thing goes wrong during reading the 2fsxA.chrg file. So I decide to verify the code I found that in the file energy/energy_react.cpp (where the chrg file is created) print out it in a format different than that it will be used do read it in site/site_writeSite.cpp file.
Then, I change the energy/energy_react.cpp to produces a output that can be read from site_writeSite.cpp and created a patch file.

Let me know if there is something more that I can do to help.

thanks.
José.

Code: Select all

diff -rupN Delphi_Linux/src/energy/energy_react.cpp Delphi_Linux-patched/src/energy/energy_react.cpp
--- Delphi_Linux/src/energy/energy_react.cpp    2015-11-15 15:25:28.000000000 -0200
+++ Delphi_Linux-patched/src/energy/energy_react.cpp    2016-01-28 18:46:51.569237184 -0200
@@ -274,7 +274,18 @@ void CDelphiEnergy::energy_react(delphi_
                     if(iSurfCrgFormatOut==1 || iSurfCrgFormatOut==2){
                                jj = atsurf[i];    //from surface construction class
                                                qq = atoi(prgapAtomPdb[jj-1].getAtInf().substr(11,4).c_str());
-                                               ofScrgFile << "ATOM  " << setw(5) << fixed << right << i+1 << " " <<  setw(5) << fixed << right << jj << " SC " << setw(6) << fixed << right << qq << "      " << setw(5) << fixed << right << prgfgSurfCrgA[i].nX << "  " << setw(5) << fixed << right << prgfgSurfCrgA[i].nY << "  " << setw(5) << fixed << right << prgfgSurfCrgA[i].nZ << "  " << setw(5) << fixed << right << scientific << fEnergy_Temp1 << "  " << setw(5) << fixed << right << scientific << spt1 << endl;
+                                               ofScrgFile << setw(6) << left << "ATOM  ";      //line(1:6)
+                                               ofScrgFile << setw(5) << right << i+1;          //line(7:11)
+                                               ofScrgFile << setw(5) << right << jj;           //line(12:16)
+                                               ofScrgFile << " SC " << setw(6) << right << qq << "    "; //line(17:30)
+                                               ofScrgFile << fixed << setprecision(3);
+                                               ofScrgFile << setw(8) << right << prgfgSurfCrgA[i].nX; //line(31:38) 8.3f
+                                               ofScrgFile << setw(8) << right << prgfgSurfCrgA[i].nY; //line(39:46) 8.3f
+                                               ofScrgFile << setw(8) << right << prgfgSurfCrgA[i].nZ; //line(47:54) 8.3f
+                                               ofScrgFile << fixed << scientific;
+                                               ofScrgFile << setw(6) << right << fEnergy_Temp1; //line(55:60) 6.3f
+                                               ofScrgFile << setw(6) << right << spt1; //line(61:66)  6.f
+                                               ofScrgFile << endl;
                                        }
                        }
                }

hesho
Posts: 3
Joined: Mon May 23, 2016 5:09 pm
Contact:

Re: [Bug] - Wrong format in I/O of site files

Post by hesho » Mon May 23, 2016 5:16 pm

i have the same problem !
Hello i am adam ... and this is my personal website http://www.adamkempfitness.com

ghudson
Posts: 3
Joined: Sat Jun 04, 2016 4:15 am

Re: [Bug] - Wrong format in I/O of site files

Post by ghudson » Sat Jun 04, 2016 4:27 am

this happens every time. Please tell the solution.

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