From MCCCM@jazz.ucc.uno.edu Sun Aug 4 17:14:26 1993 Date: 04 Aug 1993 23:14:26 -0600 (CST) From: MCCCM@jazz.ucc.uno.edu Subject: MD,discover,H-bond,help To: chemistry@ccl.net Message-Id: <01H1D56GS2CY8WWVSJ@jazz.ucc.uno.edu> Dear Netters, Could you please try to help a friend of mine with the following: I am trying to run Discover with Amber force field. It seems that the minimization makes my initial B_DNA_Duplex structure (7 nucleotide-pairs) fall apart. What should I do to avoid that? Is there a way to avoid the hydrogen bonds get apart? Here is the input file. I can send you the .car and the .mdf files if you wish to take a look -----------------------------Input file----------------------- overlap = 0.01 cutoff = 12.000000 cutdis = 11.000000 swtdis = 1.5 begin simulation * add-automatic bond torsion valence out-of-plane reduce scale 1-4 parameters by 0.500000 set dielectric = 4.000000*r Minimize * no cross terms * no morse * for 10000 iterations * using conjugate gradient * until the maximum derivative is less than 0.001000000 kcal/A end ------------------------------------------------end of input file Any help is highly appreciatted. Thanks, Monica From apa@pop.cc.adfa.oz.au Fri Aug 6 00:22:35 1993 Date: Thu, 5 Aug 1993 14:22:35 +1000 Message-Id: <199308050422.AA07827@sserve.cc.adfa.oz.au> To: chemistry@ccl.net From: apa@pop.cc.adfa.oz.au Subject: ESP-fitted charges and dipole contraints (cont...relatively long) Thanks for the several comments I've received regarding the use of the dipole moment as a constraint when fitting the esp to atom-centered point-charges, but I'm not yet convinced that there is anything "wrong" with DM-constrained esp-fits. As several respondents have pointed out, the dipole moment depends on your choice of coordinate system, but once you've made that choice for the semiemp. (or ab initio) calc of the esp, you can define a dipole moment in this coord. system, so why not constrain the point charges (which are centered on atoms with coords in the same system) to reproduce that dipole moment? A different choice of coord system would give a different dipole moment, but then the atoms would have different coords as well. It's not obvious to me that fitting the new esp, constrained to reproduce the new dipole moment, wouldn't produce the same set of point charges. In fact, a more-mathematically inclined colleague here suggests that the derived set of point charges is probably independent of coordinate system ("because the matrix you get for the least-squares fitting is invertible"??) The use of point charges in many in-house and (all?) commercial mol. modeling tools is widespread and has obvious appeal, but also important limitations. I guess a valid question to ask is why would one want to use a calculated dipole moment in the point-charge derivation? There seems to me to be two main reasons: (i) because you have an experimental observable with which to verify your calcs. (but only if the molecule is neutral), and (ii) because it's not obvious that the set of point-charges you get by esp-fitting is unique, and any extra constraint is likely to reduce the number of possible sets. This argument could be used to constrain with higher order multipoles I guess. As a matter of interest, when the check on dipole moment constraint for charged systems is disabled in the Mopac6 code, the following set of AM1-esp derived charges is available for comparison (GNORM=0.01, PRECISE keywords). The ESP and point-charge calc. x, y, z-dipole moment components are also shown. Mulliken ESP ESP no DM contraint with DM constraint NH4+ N -0.094 N -0.600 N -0.600 DHf=150.581 kcal HN +0.274 HN +0.400 HN +0.400 rrms 0.0010 rrms 0.0010 D=0.00,0.00,0.00 D=0.00,0.00,0.00 D=0.00,0.00,0.00 CH3.NH3+ N -0.059 N -0.184 N -0.716 DHf=148.748 kcal HN +0.262 HN +0.312 HN +0.54 C -0.204 C -0.329 C +0.19 HC +0.159 HC +0.192 HC -0.034 rrms 0.0080 rrms 0.1293 D=0.81,1.12,1.86 D=-0.42,-0.58,-0.96 D=0.80,1.12,1.86 (CH3)2.NH2+ N -0.028 N +0.067 N -0.060 DHf=149.215 kcal HN +0.254 HN +0.287 HN +0.400 C -0.200 C -0.489 C -0.295 HC +0.153 HC +0.211,+0.229 HC +0.097,+0.230 rrms 0.0076 rrms 0.1043 D=0.91,1.25,0.00 D=-0.73,-1.00,0.00 D=0.91,1.25,0.00 (CH3)3.NH+ N +0.004 N +0.287 N +0.392 DHf=151.997 kcal HN +0.250 HN +0.292 HN +0.329 C -0.196 C -0.587,-0.60 C -0.56,-0.63 HC +0.148 HC +0.237,+0.25 HC +0.18,+0.25 rrms 0.0045 rrms 0.0636 D=0.85,0.00,0.00 D=-0.94,0.00,0.00 D=0.85,0.00,0.00 (CH3)4N+ N +0.030 N +0.509 N +0.509 DHf=157.156 kcal C -0.187 C -0.62 C -0.62 HC +0.143 HC +0.246 HC +0.246 rrms 0.0042 rrms 0.0042 D=0.00,0.00,0.00 D=0.00,0.00,0.00 D=0.00,0.00,0.00 For those of you who are still here (it took longer to type this thing than to do the Mopac runs!) I invite comment about this table. Some comments on the table: (1) most obvious - esp-fits are numerically more precise (except for the tetrahedral examples) if DM constraint is not used. Whether the fits are "better" in a chemical sense is a moot point. (2) Unconstrained esp-derived atom-centered charges follow the poor old Mulliken charges in the organic chemist's spirit of the methyl group being an electron pusher. Magnitudes are much larger though. (3) Intriguingly, DM-constrained esp-derived point charges also follow this trend - with the glaring exception of Me2NH2+ (N is "too negative" and C is "too positive"). (4) Does anyone else think it suspicious that every non-zero point-charge-derived dipole-moment-component in the Unconstrained fits, is the *opposite* sign to the corresponding esp-derived components?? Could this be due to a change of coordinate system in the bowels of Mopac, or is this just a coincidence? The dipole-constrained Me2NH2+ fit is "poor", but all things are relative, as the corresponding table for the non-protonated, neutral amines shows: Mulliken ESP ESP no DM contraint with DM constraint NH3 N -0.396 N -0.807 N -1.130 DHf=-7.283 kcal HN +0.132 HN +0.269 HN +0.378 rrms 0.0594 rrms 0.4098 D=0.63,0.88,-1.50 D=0.44,0.63,-1.07 D=0.63,0.88,-1.50 CH3.NH2 N -0.352 N -0.708 N -0.835 DHf=-7.381 kcal HN +0.143 HN +0.280 HN +0.323 C -0.129 C +0.018 C +0.031 HC +0.03,+0.08 HC +0.00,+0.62 HC +0.05 rrms 0.205 rrms 0.4525 D=0.46,-0.73,-1.22 D=0.26,-0.48,-0.79 D=0.46,-0.73,-1.22 (CH3)2.NH N -0.308 N -0.448 N -0.518 DHf=-5.626 kcal HN +0.153 HN +0.292 HN +0.316 C -0.125 C -0.262 C -0.243 HC +0.04,+0.08 HC +0.09 to +0.14 HC +0.10 to +0.13 rrms 0.2403 rrms 0.4536 D=0.35,-0.65,-0.99 D=0.20,-0.39,-0.58 D=0.35,-0.65,-0.99 (CH3)3.N N -0.267 N -0.098 N -0.136 DHf=-1.710 kcal C -0.118 C -0.419,-0.455 C -0.38,-0.45 HC +0.04,+0.08 HC +0.14 to +0.17 HC +0.14 to +0.17 rrms 0.2054 rrms 0.4095 D=0.28,-0.50,-0.85 D=0.15,-0.27,-0.46 D=0.28,-0.50,-0.85 In this table, all the fits (constrained or not) are "very poor", but I suspect that many people wanting point charges would use these anyway! (so why not use dipole-contrained charges for charged species in the first table!!) Some food for thought... ---- Alan Arnold | e-mail: apa@pop.cc.adfa.oz.au Chem. Department,University College | voice : +61 6 268 8080 Australian Defence Force Academy | fax : +61 6 268 8002 CANBERRA ACT 2601 Australia | From tevelde@chem.vu.nl Thu Aug 5 13:44:54 1993 Message-Id: <9308051044.AA14689@gallium.chem.vu.nl> Date: Thu, 5 Aug 1993 12:44:54 +0100 To: CHEMISTRY@ccl.net From: tevelde@chem.vu.nl (Bert te Velde) Subject: duplicates I'm getting the same mailings from the mail exploder again and again,. --------------------------------------------------------- Bert te Velde, e-mail: tevelde@chem.VU.NL Department of Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, Netherlands phone: +31-(0)20-548 2978, fax: +31-(0)20-646 1479 --------------------------------------------------------- From sauer@organik.uni-erlangen.de Thu Aug 5 08:53:58 1993 From: Wolfgang Sauer Message-Id: <9308051236.AA01441@derioc1.organik.uni-erlangen.de> Subject: Queuing Sytems To: CHEMISTRY@ccl.net (CompChem MailExploder), Date: Thu, 5 Aug 93 14:36:56 METDST Dear Netters, As clusters of networked workstations are becoming ever more popular in the Comp Chem community, so do queuing systems to utilize their power such as NQS (public domain and proprietory versions), DQS, ... I'd like to hear about the experiences people have made with these systems, advantages and disadvantages of the respective systems (ease of use, performance ...). I'll summarize to the net, if there is enough interest. Wolfgang. -- +======================================+=====================================+ ! Please note the change of all German postcodes since 1 July 1993 ! +======================================+=====================================+ | Wolfgang Sauer | | | Institut fuer Organische Chemie I | "You have to be three standard | | Henkestr. 42, D-91054 Erlangen, FRG | deviations away from a normal | | | personality to like UNIX." | | sauer@organik.uni-erlangen.de | | | Tel.: 49/0 - 9131 - 85 - 2952 | Morris Jones (C&T) | | Fax: - 9132 | | +======================================+=====================================+ From XRASIMMIE@bodkin.ucg.ie Thu Aug 5 15:03:00 1993 Date: Thu, 05 Aug 1993 15:03 +0000 (GMT) From: John MacDonald Simmie Subject: modelling of oligosaccharides? To: chemistry@ccl.net Message-Id: <01H1E2J93WM88WVZRU@bodkin.ucg.ie> Hi: A colleague wants to add molecular modelling to her work on synthesis etc on "conformational aspects of oligosacch= arides" what would people recommend in terms of soft/hardware? Thanks, John ------------------------------------------------- Dr. John M. Simmie Chemistry Department Roinn na Ceimice University College Col=E1iste na hOllscoile Galway Gaillimh Ireland Eire Fax: (+353)-91-25700 F=F3n:(+353)-91-50388 ------------------------------------------------- XRASIMMIE@BODKIN.UCG.IE From cory@riemann.math.mun.ca Thu Aug 5 10:57:10 1993 Date: Thu, 5 Aug 1993 13:27:10 -0230 From: "Cory C. Pye" Message-Id: <9308051557.AA22879@riemann.math.mun.ca> To: chemistry@ccl.net Subject: Plotting ab initio molecular orbitals Hello fellow netters, I am looking for a program which can plot molecular orbitals, given a geometry, basis set, and final SCF coefficients. My requirements are 1) Preferably SGI Indigo with output to either the screen or printer (postscript, dvi). Alternatives: VAX 4500, Apollo DN10000, (VIC-20 :-)) 2) Ability to use any basis set given to it. (Not absolutely necessary) 3) Ability to use any atom defined within the basis set. (necessary) 4) Hopefully, public domain or shareware (I'm a grad student => $ = 0) 5) Easy to install. 6) Ab initio data (DFT & semiemp. would be an interesting bonus) 7) geometry: Cartesian or z-matrix(preferred) I am thinking along the lines of the program PSI/88 which I have found very useful. The code, however is heavily optimized and probably difficult to extend to arbitrary bases and atoms. It can handle atoms H-Ar and bases STO-3G, 3-21G, 6-31G with and without diffuse and polarization functions. I have used this on a VAX 4500. There is a program xpsi of which I am aware (basically the above with application of f2c and using PEX libraries) if I am not mistaken. Alternatively, somebody could tell me the status of PEX on the SGI, and if free, an ftp site where one could obtain this. This of course does not solve my problem of wishing to print molecules with atoms larger than Ar. I suspect that there may be some Explorer modules or some extension of programs like xmol which may be able to do this. Remember, free is the key word. I do not want to envision the idea of writing it myself, except as a last resort, since I program in OSIPE-Fortran ('Fortran++') and I would probably have to learn C (C++) to take advantage of the full capabilities of X/Motif, GL, or PEX. Please send replies to cory@riemann.math.mun.ca (as in header) or if this fails try cory@kean.ucs.mun.ca cory@morgan.ucs,mun.ca cory@zeus.chem.mun.ca cory@bohr.chem.mun.ca I will try to post a summary. -Cory Pye