From owner-chemistry@ccl.net Fri Jul 15 02:54:07 2005 From: "CCL" To: CCL Subject: CCL: W:pdbqtopdb problem Message-Id: <-28893-050715020356-30230-gJKokDZHWSap5rm98+rrIw{=}server.ccl.net> X-Original-From: "Farzin Hadizadeh" Sent to CCL by: "Farzin Hadizadeh" Dear Sir, I am now using Autodock5.0. I want to add the macromolecule and the docked conformations together into one PDB file that contains everything. % pdbqtopdb mymacromolecule.pdbqs >> mydocking.dlg.pdb However, when I run pdbqtopdb command, the error information is displayed: ---------------------------------------------------------- % pdbqtopdb 3ptb.pdbqs >> benA.3ptb.dlg.pdb awk: /home/xiong/autodock/dist305/share/pdbtopdb2.awk:49: fatal: Invalid range end: /[0-9][+- ]/ /home/xiong/autodock/dist305/share/fixatomnames: line 8: 4340 M Ic {_ sed -f AUTODOC K_UTI/fixatomnames.sed * /home/xiong/autodock/dist305/share/getpdbrecords: line 2: 4338 M Ic {_ egrep "^ATOM|^ HETATM|^REMARK|^USER|^END |^TER|^MODEL |^ENDMDL" * ---------------------------------------------------------------- Could you please tell me why I can't get the pdb file contain the macromolecule and the docked ligand conformations? From owner-chemistry@ccl.net Fri Jul 15 03:05:30 2005 From: "CCL" To: CCL Subject: CCL: W:pdbqtopdb problem Message-Id: <-28894-050715020356-30230-gJKokDZHWSap5rm98+rrIw[-]server.ccl.net> X-Original-From: "Farzin Hadizadeh" Sent to CCL by: "Farzin Hadizadeh" Dear Sir, I am now using Autodock5.0. I want to add the macromolecule and the docked conformations together into one PDB file that contains everything. % pdbqtopdb mymacromolecule.pdbqs >> mydocking.dlg.pdb However, when I run pdbqtopdb command, the error information is displayed: ---------------------------------------------------------- % pdbqtopdb 3ptb.pdbqs >> benA.3ptb.dlg.pdb awk: /home/xiong/autodock/dist305/share/pdbtopdb2.awk:49: fatal: Invalid range end: /[0-9][+- ]/ /home/xiong/autodock/dist305/share/fixatomnames: line 8: 4340 M Ic {_ sed -f AUTODOC K_UTI/fixatomnames.sed * /home/xiong/autodock/dist305/share/getpdbrecords: line 2: 4338 M Ic {_ egrep "^ATOM|^ HETATM|^REMARK|^USER|^END |^TER|^MODEL |^ENDMDL" * ---------------------------------------------------------------- Could you please tell me why I can't get the pdb file contain the macromolecule and the docked ligand conformations? From owner-chemistry@ccl.net Fri Jul 15 20:54:09 2005 From: "CCL" To: CCL Subject: CCL: CIS-MP2 calculation Message-Id: <-28895-050715111518-32204-gJKokDZHWSap5rm98+rrIw^^^server.ccl.net> X-Original-From: "ilsun" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0000_01C5898E.03CEE820" MIME-Version: 1.0 Sent to CCL by: "ilsun" This is a multi-part message in MIME format. ------=_NextPart_000_0000_01C5898E.03CEE820 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear All, I'm a novice at the Gaussian computation. I want to know the way to do CIS-MP2 calculation for calibration energy values by CIS calculation using Gaussian03. Please let me know this method ^^.. Thank you in advance, Ilsun Yoon ------=_NextPart_000_0000_01C5898E.03CEE820 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear = All,

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I’= ;m a novice at the Gaussian computation.

&n= bsp;

I want = to know the way to do CIS-MP2 calculation for calibration energy values by = CIS calculation using Gaussian03.

&n= bsp;

Please = let me know this method ^^.. =

&n= bsp;

Thank = you in advance,

&n= bsp;

Ilsun Yoon

&n= bsp;

 

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