From owner-chemistry@ccl.net Tue Feb 6 12:54:00 2018 From: "SM Bargeen Turzo smbargeen.turzo.2016/a\owu.edu" To: CCL Subject: CCL: Geometry Opt of a QM/MM system in QuanPol Message-Id: <-53169-180206125151-32070-d9U3LFxl3PWwNHnZ/vgSdw]-[server.ccl.net> X-Original-From: "SM Bargeen Turzo" Date: Tue, 6 Feb 2018 12:51:50 -0500 Sent to CCL by: "SM Bargeen Turzo" [smbargeen.turzo.2016 ~ owu.edu] Hi all, I am trying to geometry optimize a large protein(1192 atoms including water molecules and a small organic molecule) in QuanPol I got the geometry to optimize in 2844 steps with the following inputs: ################################################################################## ! CHT, Cyr489, Glu 491 in QM. MM RESIDUES WITHIN 10A OF CHT $CONTRL SCFTYP=UHF RUNTYP=OPTIMIZE MULT=2 ICHARG=0 MAXIT=200 $END $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END $SCF DIRSCF=.T. SOSCF=.T. $END $SYSTEM MWORDS=60 MEMDDI=1.25 PARALL=.TRUE. $END $STATPT METHOD=NR OPTTOL=0.0008 $END $QUANPO LJQMMM=0 NSTEP=100000 JOUT=100 KOUT=1000 ITYPWAT=304 SWRA=10 SWRB=12 IHESS=0 SWRAQ=22 SWRBQ=32 NFFTYP=20000 NFFFILE=2 TOPFILE= './par_top/top_all36_prot.rtf' PARFILE= './par_top/par_all36_prot.prm' $END ################################################################################## However at the start of the QuanPol calculation I am seeing this error: ################################################################################## ################################################################################## ERROR: ATOM 7 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. WARNING: ATOM 36 FORMS NO BOND. ERROR: ATOM 59 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. WARNING: ATOM 126 FORMS NO BOND. ERROR: ATOM 145 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. WARNING: ATOM 209 FORMS NO BOND. ERROR: ATOM 231 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. WARNING: ATOM 263 FORMS NO BOND. WARNING: ATOM 277 FORMS NO BOND. ERROR: ATOM 295 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. WARNING: ATOM 327 FORMS NO BOND. ERROR: ATOM 346 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. WARNING: ATOM 425 FORMS NO BOND. WARNING: ATOM 439 FORMS NO BOND. WARNING: ATOM 456 FORMS NO BOND. WARNING: ATOM 470 FORMS NO BOND. ERROR: ATOM 492 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. WARNING: ATOM 585 FORMS NO BOND. ERROR: ATOM 608 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. WARNING: ATOM 689 FORMS NO BOND. WARNING: ATOM 710 FORMS NO BOND. WARNING: ATOM 780 FORMS NO BOND. ERROR: ATOM 805 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. WARNING: ATOM 885 FORMS NO BOND. ERROR: ATOM 904 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. WARNING: ATOM 942 FORMS NO BOND. WARNING: ATOM 958 FORMS NO BOND. ERROR: ATOM 983 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. WARNING: ATOM 1053 FORMS NO BOND. WARNING: ATOM 1061 FORMS NO BOND. WARNING: ATOM 1062 FORMS NO BOND. WARNING: ATOM 1063 FORMS NO BOND. WARNING: ATOM 1064 FORMS NO BOND. WARNING: ATOM 1065 FORMS NO BOND. WARNING: ATOM 1066 FORMS NO BOND. WARNING: ATOM 1067 FORMS NO BOND. ERROR: ATOM 1068 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. ERROR: ATOM 1069 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. ERROR: ATOM 1070 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. ERROR: ATOM 1071 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. ERROR: ATOM 1072 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. ERROR: ATOM 1073 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. ERROR: ATOM 1074 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. ERROR: ATOM 1075 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. ERROR: ATOM 1076 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. ERROR: ATOM 1077 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. ERROR: ATOM 1078 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. ERROR: ATOM 1079 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. ERROR: ATOM 1080 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. ERROR: ATOM 1081 FORMS NO BOND. THE BOND LENGTH MAY BE TOO LONG, OR THE H IS ATTACHED TO A WRONG O OR N ATOM IN PDB. ################################################################################## ################################################################################## ################################################################################## My questions are : Q1) How worried should I be of these errors? Q2) Should I do an MM energy minimization before QM/MM opt? if no to Q2. Q3) What other approach should I be looking into to fix these error? Any help will be greatly appreciated. -Bargeen From owner-chemistry@ccl.net Tue Feb 6 13:29:01 2018 From: "Manish Sud msud+/-san.rr.com" To: CCL Subject: CCL: New release of MayaChemTools Message-Id: <-53170-180206132559-10501-GerpU6gmzAlDMyLu3Y2xJw .. server.ccl.net> X-Original-From: "Manish Sud" Date: Tue, 6 Feb 2018 13:25:58 -0500 Sent to CCL by: "Manish Sud" [msud===san.rr.com] Hi All, A new release of MayaChemTools, a growing collection of Perl and Python scripts, is now available containing the following command line Python scripts based on RDKit: o RDKitCalculateMolecularDescriptors.py o RDKitCalculateRMSD.py o RDKitClusterMolecules.py o RDKitCompareMoleculeShapes.py o RDKitConvertFileFormat.py o RDKitDrawMolecules.py o RDKitEnumerateCompoundLibrary.py o RDKitEnumerateStereoisomers.py o RDKitFilterPAINS.py o RDKitGenerateConformers.py o RDKitGenerateMolecularFrameworks.py o RDKitPerformMinimization.py o RDKitPickDiverseMolecules.py o RDKitRemoveDuplicateMolecules.py o RDKitSearchFunctionalGroups.py o RDKitSearchSMARTS.py The core set of command line Perl scripts available in MayaChemTools has no external dependencies. A variety of enhancements have been made to these core scripts. The Python scripts based on RDKit rely on its availability in your environment. These scripts have been tested using the latest release of RDKit available for both Anaconda2 and Anaconda3, and appear to work as expected. Please visit www.MayaChemTools.org for further details. Your feedback is welcome. Manish Sud msud|a|san.rr.com www.MayaChemTools.org From owner-chemistry@ccl.net Tue Feb 6 16:10:00 2018 From: "Sherrill, Charles D sherrill^chemistry.gatech.edu" To: CCL Subject: CCL: Georgia Tech Summer Theory Program Message-Id: <-53171-180206145254-27205-AvDr9vTG4KwALzPWWa6tVg]^[server.ccl.net> X-Original-From: "Sherrill, Charles D" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_SN4PR0701MB3789A671E1823C1623620B1DE3FD0SN4PR0701MB3789_" Date: Tue, 6 Feb 2018 19:52:47 +0000 MIME-Version: 1.0 Sent to CCL by: "Sherrill, Charles D" [sherrill_._chemistry.gatech.edu] --_000_SN4PR0701MB3789A671E1823C1623620B1DE3FD0SN4PR0701MB3789_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Georgia Tech will host its annual Summer Theory Program as part of its NSF-sponsored Research Experiences for Undergraduates (REU) program in chemistry and biochemistry. The ten-week program runs from May 21 to July 28 and is open to students who will be in their junior or senior years during the next academic year. Theory students will work with Professors Jesse McDaniel, David Sherrill, or Jean-Luc Bredas in the areas = of statistical mechanics, electronic structure theory, or organic electronics. The research experience is supplemented by an introductory lecture series in theoretical chemistry. Successful applicants will receive a stipend of $5000, a travel allowance, and housing. Further details are available at http://vergil.chemistry.gatech.edu/opp/summer.html and http://ww2.chemistry.gatech.edu/reu/ Participants supported by the NSF must be US citizens or permanent resident= s of the US. The deadline for applications is February 15. --_000_SN4PR0701MB3789A671E1823C1623620B1DE3FD0SN4PR0701MB3789_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Georgia Tech will host its annual Summer Theory Program as part of its=
NSF-sponsored Research Experiences for Undergraduates (REU) program in=
chemistry and biochemistry.  The ten-week program runs from May 2= 1 to
July 28 and is open to students who will be in their junior or senior<= /div>
years during the next academic year.  Theory students will work w= ith
Professors Jesse McDaniel, David Sherrill, or Jean-Luc Bredas in the a= reas of
statistical mechanics, electronic structure theory, or organic electro= nics.
The research experience is supplemented by an introductory lecture
series in theoretical chemistry.  Successful applicants will rece= ive
a stipend of $5000, a travel allowance, and housing.  Further det= ails
are available at

   http://vergil.chemistry.gatech.edu/opp/summer.html
and
   http://ww2.chemistry.gatech.edu/reu/

Participants supported by the NSF must be US citizens or permanent res= idents
of the US.

The deadline for applications is February 15.

--_000_SN4PR0701MB3789A671E1823C1623620B1DE3FD0SN4PR0701MB3789_--