acpypi - Project Hosting on Google Code

Last 7 days Dec 22, 2009 r263 (ready for AmberTools 1.3 and support for divcon, mopac or sq...) committed by alanwilter - ready for AmberTools 1.3 and support for divcon, mopac or sqm. ready for AmberTools 1.3 and support for divcon, mopac or sqm. Dec 22, 2009 Tutorial_MD Wiki page deleted by alanwilter - Revision r262 [No log message] Revision r262 [No log message] Dec 22, 2009 3 Wiki pages changed by alanwilter - Revision r261 Update doc to reflect AmberTools 1.3 Added Tutorial_MD Edited HowAcpypiWorks">HowAcpypiWorks, HowToUse">HowToUse Revision r261 Update doc to reflect AmberTools 1.3 Added Tutorial_MD Edited HowAcpypiWorks">HowAcpypiWorks, HowToUse">HowToUse Last 30 days Dec 11, 2009 r260 (test updates) committed by alanwilter - test updates test updates Nov 30, 2009 Thanks (Contributions & Feedbacks) Wiki page edited by alanwilter - Revision r259 updated Thanks.wiki Revision r259 updated Thanks.wiki Nov 30, 2009 r258 (Class Atom now stores charge converted and not doing convers...) committed by alanwilter - Class Atom now stores charge converted and not doing conversion within it. Solved the bug spotted by David Wright when using acpypi as amb2gmx. Class Atom now stores charge converted and not doing conversion within it. Solved the bug spotted by David Wright when using acpypi as amb2gmx. Earlier this year Oct 22, 2009 Thanks (Contributions & Feedbacks) Wiki page edited by alanwilter - Revision r257 updated Thanks.wiki Revision r257 updated Thanks.wiki Oct 22, 2009 r256 (charge in gmx itp/top with 6 digits of precision instead of ...) committed by alanwilter - charge in gmx itp/top with 6 digits of precision instead of 5 charge in gmx itp/top with 6 digits of precision instead of 5 Oct 20, 2009 HowAcpypiWorks (ACPYPI under the bonnet) Wiki page edited by alanwilter - Revision r255 Edited wiki page through web user interface. Revision r255 Edited wiki page through web user interface. Oct 20, 2009 HowAcpypiWorks (ACPYPI under the bonnet) Wiki page edited by alanwilter - Revision r254 Edited wiki page through web user interface. Revision r254 Edited wiki page through web user interface. Sep 09, 2009 r253 (to allow wget, although svn is the correct way of downloadin...) committed by alanwilter - to allow wget, although svn is the correct way of downloading acpypi to allow wget, although svn is the correct way of downloading acpypi Aug 24, 2009 2 Wiki pages changed by alanwilter - Revision r252 update wiki Edited Thanks, TutorialAcpypi4Gromacs">TutorialAcpypi4Gromacs Revision r252 update wiki Edited Thanks, TutorialAcpypi4Gromacs">TutorialAcpypi4Gromacs Aug 23, 2009 TutorialAcpypi4Gromacs (An example illustrating how to use ACPYPI with GROMACS) Wiki page commented on by alanwilter - No. The whole point is to get the topology of your ligand, but the way acpypi works it will only give topology for insulated molecules, i.e., not covalent bonded to the protein. But it is possible to figure out a way of doing what you asked but I am afraid it's not simple, let alone, straightforward. No. The whole point is to get the topology of your ligand, but the way acpypi works it will only give topology for insulated molecules, i.e., not covalent bonded to the protein. But it is possible to figure out a way of doing what you asked but I am afraid it's not simple, let alone, straightforward. Jul 19, 2009 r251 (improved resname detection, keep mopac.pdb and mopac.out) committed by alanwilter - improved resname detection, keep mopac.pdb and mopac.out improved resname detection, keep mopac.pdb and mopac.out Jul 08, 2009 r250 ([No log message]) committed by alanwilter - [No log message] [No log message] Jul 03, 2009 r249 (improved CcpnToAcpypi.py) committed by alanwilter - improved CcpnToAcpypi.py improved CcpnToAcpypi.py Jul 02, 2009 r248 ([No log message]) committed by alanwilter - [No log message] [No log message] Jul 02, 2009 r247 ([No log message]) committed by alanwilter - [No log message] [No log message] Jul 02, 2009 r246 ([No log message]) committed by alanwilter - [No log message] [No log message] Jul 02, 2009 r245 (improved resname allowed criteria) committed by alanwilter - improved resname allowed criteria improved resname allowed criteria Jun 23, 2009 r244 (chargeVal can be either int or str.) committed by alanwilter - chargeVal can be either int or str. chargeVal can be either int or str. Jun 17, 2009 TutorialAcpypi4Gromacs (An example illustrating how to use ACPYPI with GROMACS) Wiki page edited by alanwilter Jun 05, 2009 r242 (working for K+ for amb2gmx emulation) committed by alanwilter - working for K+ for amb2gmx emulation working for K+ for amb2gmx emulation Jun 04, 2009 Thanks (Contributions & Feedbacks) Wiki page edited by alanwilter Jun 04, 2009 Thanks (Contributions & Feedbacks) Wiki page added by alanwilter Jun 04, 2009 r239 (mol and mdl format accepted without babel) committed by alanwilter - mol and mdl format accepted without babel mol and mdl format accepted without babel Jun 04, 2009 FAQ (Frequent Asked Questions about ACPYPI) Wiki page edited by alanwilter Jun 04, 2009 FAQ (Frequent Asked Questions about ACPYPI) Wiki page edited by alanwilter Jun 04, 2009 r236 (improved antechamber detection and angle and dih generated a...) committed by alanwilter - improved antechamber detection and angle and dih generated anyway for cns. improved antechamber detection and angle and dih generated anyway for cns. Jun 03, 2009 HowAcpypiWorks (ACPYPI under the bonnet) Wiki page edited by alanwilter May 15, 2009 r234 ('_' for CNS atomTypes and no OPLS when amb2gmx-like) committed by alanwilter - '_' for CNS atomTypes and no OPLS when amb2gmx-like '_' for CNS atomTypes and no OPLS when amb2gmx-like May 15, 2009 3 Wiki pages changed by alanwilter - Edited TutorialAcpypi4Gromacs">TutorialAcpypi4Gromacs, TutorialAcpypi4GromacsOPLS">TutorialAcpypi4GromacsOPLS, TutorialNAMD Edited TutorialAcpypi4Gromacs">TutorialAcpypi4Gromacs, TutorialAcpypi4GromacsOPLS">TutorialAcpypi4GromacsOPLS, TutorialNAMD May 12, 2009 HowAcpypiWorks (ACPYPI under the bonnet) Wiki page edited by alanwilter May 11, 2009 r231 (- imporvement for OPLS) committed by alanwilter - - imporvement for OPLS - imporvement for OPLS May 11, 2009 HowAcpypiWorks (ACPYPI under the bonnet) Wiki page edited by alanwilter May 11, 2009 4 Wiki pages changed by alanwilter - Edited HowAcpypiWorks">HowAcpypiWorks, TutorialAcpypi4Gromacs">TutorialAcpypi4Gromacs, TutorialAcpypi4GromacsOPLS">TutorialAcpypi4GromacsOPLS, TutorialNAMD Edited HowAcpypiWorks">HowAcpypiWorks, TutorialAcpypi4Gromacs">TutorialAcpypi4Gromacs, TutorialAcpypi4GromacsOPLS">TutorialAcpypi4GromacsOPLS, TutorialNAMD May 07, 2009 HowAcpypiWorks (ACPYPI under the bonnet) Wiki page edited by alanwilter May 07, 2009 HowAcpypiWorks (ACPYPI under the bonnet) Wiki page edited by alanwilter May 07, 2009 HowAcpypiWorks (ACPYPI under the bonnet) Wiki page edited by alanwilter May 07, 2009 HowAcpypiWorks (ACPYPI under the bonnet) Wiki page edited by alanwilter May 06, 2009 r224 ([No log message]) committed by alanwilter - [No log message] [No log message] May 06, 2009 r223 (doc update) committed by alanwilter - doc update doc update May 06, 2009 HowAcpypiWorks (ACPYPI under the bonnet) Wiki page edited by alanwilter May 06, 2009 2 Wiki pages changed by alanwilter - Edited HowAcpypiWorks">HowAcpypiWorks, TutorialAcpypi4Gromacs">TutorialAcpypi4Gromacs Edited HowAcpypiWorks">HowAcpypiWorks, TutorialAcpypi4Gromacs">TutorialAcpypi4Gromacs May 06, 2009 Tutorial_MD Wiki page deleted by alanwilter May 06, 2009 6 Wiki pages changed by alanwilter - Added Tutorial_MD Edited HowAcpypiWorks">HowAcpypiWorks, HowToUse">HowToUse, TutorialAcpypi4Gromacs">TutorialAcpypi4Gromacs, TutorialAcpypi4GromacsOPLS">TutorialAcpypi4GromacsOPLS, TutorialNAMD Added Tutorial_MD Edited HowAcpypiWorks">HowAcpypiWorks, HowToUse">HowToUse, TutorialAcpypi4Gromacs">TutorialAcpypi4Gromacs, TutorialAcpypi4GromacsOPLS">TutorialAcpypi4GromacsOPLS, TutorialNAMD May 06, 2009 FAQ (Frequent Asked Questions about ACPYPI) Wiki page edited by alanwilter May 06, 2009 4 Wiki pages changed by alanwilter - Added TutorialAcpypi4GromacsOPLS">TutorialAcpypi4GromacsOPLS Edited HowAcpypiWorks">HowAcpypiWorks, HowToUse">HowToUse, TutorialAcpypi4Gromacs">TutorialAcpypi4Gromacs Added TutorialAcpypi4GromacsOPLS">TutorialAcpypi4GromacsOPLS Edited HowAcpypiWorks">HowAcpypiWorks, HowToUse">HowToUse, TutorialAcpypi4Gromacs">TutorialAcpypi4Gromacs May 05, 2009 r216 (- imporvement for OPLS) committed by alanwilter - - imporvement for OPLS - imporvement for OPLS May 01, 2009 r215 (- experimental OPLS/AA generation, derived via dictionaries ...) committed by alanwilter - - experimental OPLS/AA generation, derived via dictionaries from amber and gaff atom types. - removed bcc and sybyl atomtypes: useless - experimental OPLS/AA generation, derived via dictionaries from amber and gaff atom types. - removed bcc and sybyl atomtypes: useless

TutorialAcpypi4Gromacs (An example illustrating how to use ACPYPI with GROMACS) Wiki page commented on by alanwilter - No. The whole point is to get the topology of your ligand, but the way acpypi works it will only give topology for insulated molecules, i.e., not covalent bonded to the protein. But it is possible to figure out a way of doing what you asked but I am afraid it's not simple, let alone, straightforward.

No. The whole point is to get the topology of your ligand, but the way acpypi works it will only give topology for insulated molecules, i.e., not covalent bonded to the protein. But it is possible to figure out a way of doing what you asked but I am afraid it's not simple, let alone, straightforward.

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