From chemistry-request@server.ccl.net Mon Jan 27 09:09:40 2003 Received: from lauca.usach.cl ([158.170.64.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0RE9cP27667 for ; Mon, 27 Jan 2003 09:09:39 -0500 Received: from danilo ([158.170.51.186]) by lauca.usach.cl (8.11.6/8.11.6) with SMTP id h0RE1mn32062 for ; Mon, 27 Jan 2003 11:01:48 -0300 From: "Danilo Gonzalez" To: Subject: dipole in InsightII Date: Mon, 27 Jan 2003 11:08:17 -0300 Message-ID: <000201c2c60d$8a76a120$ba33aa9e@usach.cl> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal Hi all!, I'm using insightII for calculate the dipole to a subset of atoms. I can obtain a nice representation of the dipole vector using Decipher module, but I can't obtain the value of that dipole. Any body have some tips for obtain the magnitude of the dipole?... if it is no possible, How I can calculate the dipole to a subset of amino acid in a protein? (Using insightII or another program) Thanks a lot for any help or comment. Dr. Danilo Gonzalez University of Santiago of Chile Faculty of Chemistry and Biology Casilla 40, Correo 33, Santiago - Chile. From chemistry-request@server.ccl.net Mon Jan 27 06:58:21 2003 Received: from marilyn.uochb.cas.cz ([147.231.120.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0RBwKP23616 for ; Mon, 27 Jan 2003 06:58:20 -0500 Received: from iveta.uochb.cas.cz (iveta.uochb.cas.cz [147.231.120.176]) by marilyn.uochb.cas.cz (8.11.6/8.11.0) with ESMTP id h0RBwIW26006; Mon, 27 Jan 2003 12:58:19 +0100 Received: by iveta.uochb.cas.cz (Postfix, from userid 501) id 3424473DFF; Mon, 27 Jan 2003 12:58:15 +0100 (CET) Date: Mon, 27 Jan 2003 12:58:15 +0100 From: Daniel Svozil To: chemistry@ccl.net Cc: Iman_boukhobza@zu.ac.ae Subject: Re: CCL:Dihedral angles Message-ID: <20030127115815.GA25690@iveta.uochb.cas.cz> References: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="SUOF0GtieIMvvwua" Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.4i --SUOF0GtieIMvvwua Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Hi Iman, > I am trying to create a z matrix for a vandium complex. I have the necessary bond lengths and angles that I got from crystallography data. The problem now is dihedral angles! > > Any idea how these angles can be found? > Dihedral angle is given for four atoms ijkl, and it is an angle between the planes given by ijk and jkl atoms. The angle between two planes is the angle between their normal vectors. Normal vector is a vector perpendicular to the plane, and it is given as a vector product of two vectors (three points - atoms give those two vectors). When calculating normal vector, the two vectors in plane may be formed as ij, jk, or as ji, jk. Those two numberings give two normal vectors that are same except for the sign. In quantum chemistry packages the ij - jk direction is used by convention. Also by convention, the dihedral angle is positive when the atom l lies in the same half-space as the normal vector of the ijk plane. This is just a short description, attached you may find a dihedral.ps file (I hope it will make it throught the system) with equations needed to calculate the dihedral angle. 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Fh(and)31=0Ab Fg(jkl)= 42 b Fh(atoms.)g(The)33 b(angle)e(b)s(et)m(w)m(een)j(t)m(w)m=0A(o)e(planes)= g(is)f(giv)m(en)h(as)257 2104 y(an)e(angle)g(b)s(et)m(w)m=0A(een)i(their)d(= normal)f(v)m(ectors.)45 b(Normal)28 b(v)m(ector)j(is)e=0A(a)h(v)m(ector)h(p= )s(erp)s(endic-)257 2225 y(ular)c(to)g(the)h(plane)f=0A(calculated)g(as)h(a= )f(v)m(ector)i(pro)s(duct)f(of)f(t)m(w)m(o)h(v)m=0A(ectors)h(\(three)f(p)s(= oin)m(ts)g(-)257 2345 y(atoms)j(giv)m(e)h(t)m=0A(w)m(o)h(v)m(ectors)g(that)= f(are)g(used)h(to)f(calculate)f(the)h=0A(normal)e(v)m(ector\).)44 b(When)25= 7 2476 y(calculating)29=0Ab(normal)g(v)m(ector,)j(the)g(t)m(w)m(o)f(v)m(ect= ors)i(in)d(plane)g(ma)=0Am(y)h(b)s(e)g(formed)f(as)3238 2453 y Ff(~)3231 24= 76=0Ay(ij)6 b Fh(,)3386 2449 y Ff(~)3368 2476 y(j)g(k)s Fh(,)257=0A2596 y(o= r)37 b(as)512 2574 y Ff(~)504 2596 y(j)6 b(i)q=0AFh(,)666 2570 y Ff(~)648 2= 596 y(j)g(k)s Fh(.)56 b(Those)38=0Ab(t)m(w)m(o)f(n)m(um)m(b)s(erings)g(giv)= m(e)f(t)m(w)m(o)i(normal)c(v)m=0A(ectors)k(that)f(are)f(same)257 2717 y(exc= ept)g(for)e(the)g(sign.)48=0Ab(In)34 b(quan)m(tum)g(c)m(hemistry)h(pac)m(k)= -5 b(ages)35=0Ab(the)g Ff(ij)29 b Fe(\000)24 b Ff(j)6 b(k)37 b Fh(direction= )c(is)257=0A2837 y(used)h(b)m(y)g(con)m(v)m(en)m(tion.)44 b(Also)32=0Ab(b)m= (y)i(con)m(v)m(en)m(tion,)g(the)f(dihedral)e(angle)h(is)g(p)s=0A(ositiv)m(e= )g(when)257 2957 y(the)h(atom)f Fg(l)42 b=0AFh(lies)32 b(in)g(the)h(same)f(= half-space)g(as)h(the)g(normal)e(v)m=0A(ector)i(of)f(the)h Fg(ijk)43 b Fh(p= lane.)404 3198 y(The)33=0Ab(normal)e(v)m(ector)i(of)g(the)g Fg(ijk)42 b Fh(= plane)33=0Ab(is)f(giv)m(en)g(as)h(a)f(v)m(ector)i(pro)s(duct:)1582=0A3405 y= Ff(n)1640 3420 y Fd(ij)t(k)1766 3405 y Fh(=3D)1878=0A3383 y Ff(~)1870 3405= y(ij)28 b Fe(\002)2089 3379 y Ff(~)2071=0A3405 y(j)6 b(k)1203 b Fh(\(1\))2= 57 3626 y(where)34 b(the)f(v)m(ectors)=0A1046 3603 y Ff(~)1038 3626 y(ij)39= b Fh(and)1358 3599=0Ay Ff(~)1340 3626 y(j)6 b(k)35 b Fh(are)e(calculated)f= (as)1113=0A3811 y Ff(~)1105 3833 y(ij)i Fh(=3D)28 b([\()p Ff(j)1421=0A3848 = y Fd(x)1487 3833 y Fe(\000)23 b Ff(i)1620 3848 y=0AFd(x)1664 3833 y Fh(\))p= Ff(;)17 b Fh(\()p Ff(j)1824=0A3848 y Fd(y)1887 3833 y Fe(\000)23 b Ff(i)20= 20 3848 y=0AFd(y)2062 3833 y Fh(\))p Ff(;)17 b Fh(\()p Ff(j)2222=0A3848 y F= d(z)2284 3833 y Fe(\000)22 b Ff(i)2416 3848 y=0AFd(z)2456 3833 y Fh(\)])850= b(\(2\))1067 3965 y Ff(~)1049=0A3991 y(j)6 b(k)30 b Fh(=3D)e([\()p Ff(k)13= 96 4006 y Fd(x)1462=0A3991 y Fe(\000)22 b Ff(j)1601 4006 y Fd(x)1646 3991 y= =0AFh(\))p Ff(;)17 b Fh(\()p Ff(k)1817 4006 y Fd(y)1879=0A3991 y Fe(\000)23= b Ff(j)2019 4006 y Fd(y)2061 3991 y=0AFh(\))p Ff(;)17 b Fh(\()p Ff(k)2232 = 4006 y Fd(z)2293=0A3991 y Fe(\000)23 b Ff(j)2433 4006 y Fd(z)2473 3991 y=0A= Fh(\)])833 b(\(3\))257 4212 y(The)34 b(v)m(ector)g(pro)s(duct)e(b)s(et)=0Am= (w)m(een)j(t)m(w)m(o)e(v)m(ectors)28 b Ff(~)-43 b(a)33=0Ab Fh(and)2270 4185= y Ff(~)2282 4212 y(b)g Fh(is)f(giv)m(en)h(b)m(y:)905=0A4419 y Ff(~)-43 b(a= )22 b Fe(\002)1072 4393 y Ff(~)1084=0A4419 y(b)28 b Fh(=3D)g(\()p Ff(a)1346= 4434 y Fd(y)1387=0A4419 y Ff(b)1428 4434 y Fd(z)1491 4419 y Fe(\000)22 b= =0AFf(a)1641 4434 y Fd(z)1681 4419 y Ff(b)1722 4434 y Fd(y)1764=0A4419 y Ff= (;)17 b(a)1859 4434 y Fd(z)1899 4419 y Ff(b)1940=0A4434 y Fd(x)2006 4419 y = Fe(\000)23 b Ff(a)2157 4434 y=0AFd(x)2201 4419 y Ff(b)2242 4434 y Fd(z)2282= 4419 y Ff(;)17=0Ab(a)2377 4434 y Fd(x)2421 4419 y Ff(b)2462 4434 y Fd(y)25= 26=0A4419 y Fe(\000)23 b Ff(a)2677 4434 y Fd(y)2718 4419 y=0AFf(b)2759 4434= y Fd(x)2804 4419 y Fh(\))529 b(\(4\))257=0A4626 y(The)34 b(normal)c(v)m(ec= tor)k(of)e(the)h Fg(jkl)43=0Ab Fh(plane)32 b(is)g(calculated)g(similarly:)1= 580 4834=0Ay Ff(n)1638 4849 y Fd(j)t(k)r(l)1762 4834 y Fh(=3D)1884=0A4807 y= Ff(~)1866 4834 y(j)6 b(k)25 b Fe(\002)2098 4807=0Ay Ff(~)2088 4834 y(k)s(l= )1200 b Fh(\(5\))404 5041 y(Once)27=0Ab(the)g(normal)d(v)m(ectors)k(are)f(k= no)m(wn,)i(the)e(angle)e(b)s(et)m=0A(w)m(een)k(the)e(planes)f(is)g(giv)m(en= )257 5161 y(b)m(y:)1288=0A5338 y Ff(\036)1346 5353 y Fd(ij)t(k)r(l)1495 533= 8 y=0AFh(=3D)h Ff(ar)s(ccos)1890 5192 y Fc( )1982 5271 y Ff(~)-46=0Ab(n)204= 3 5286 y Fd(ij)t(k)2164 5271 y Fe(\001)19 b Ff(~)-46=0Ab(n)2272 5286 y Fd(j= )t(k)r(l)p 1965 5315 424 4 v 1965=0A5407 a Fe(j)m Ff(~)g(n)2051 5422 y Fd(i= j)t(k)2150 5407=0Ay Fe(jj)m Ff(~)g(n)2264 5422 y Fd(j)t(k)r(l)2361 5407=0Ay= Fe(j)2398 5192 y Fc(!)3371 5338 y Fh(\(6\))1852 5637=0Ay(1)p eop=0A%%Page:= 2 2=0A2 1 bop 404 573 a Fh(T)-8 b(o)44 b(\014nd)g(a)g(sign)f(of)h(the)g=0A= (dihedral)f(angle)g(the)i(general)e(equation)h(of)f(the)i(plane)257=0A693 y= Ff(Ax)26 b Fh(+)e Ff(B)5 b(y)29 b Fh(+)24 b Ff(C)7=0Ab(z)30 b Fh(+)25 b Ff= (D)37 b Fh(=3D)d(0)i(m)m(ust)h(b)s(e)g(kno)m(wn.)56=0Ab(The)38 b(co)s(e\016= cien)m(ts)g Ff(A)p Fh(,)f Ff(B)5=0Ab Fh(,)38 b(and)f Ff(C)43 b Fh(are)257 8= 14 y(the)38 b(elemen)m(ts)g(of)=0Ae(the)i(normal)d(v)m(ector)k(of)d(the)i(g= iv)m(en)f(plane,)h(the)g=0AFf(D)i Fh(co)s(e\016cien)m(t)e(can)257 934 y(eas= ily)30=0Ab(b)s(e)g(calculated)f(b)m(y)i(substituting)f(the)g(co)s(ordinates= )g=0A(of)g(an)m(y)g(p)s(oin)m(t)g(lying)e(in)i(the)257 1054=0Ay(plane)j(\(e= .g.)43 b Ff(i)p Fh(\):)1168 1175 y Ff(D)30=0Ab Fh(=3D)d Fe(\000)p Fh(\()m F= f(~)-46 b(n)1555 1190 y Fd(ij)t(k)1651=0A1207 y Fb(x)1694 1175 y Ff(i)1727 = 1190 y Fd(x)1793 1175=0Ay Fh(+)19 b Ff(~)-46 b(n)1949 1190 y Fd(ij)t(k)2045= 1207=0Ay Fb(y)2086 1175 y Ff(i)2119 1190 y Fd(y)2183 1175 y=0AFh(+)19 b Ff= (~)-46 b(n)2339 1190 y Fd(ij)t(k)2434 1207=0Ay Fb(z)2474 1175 y Ff(i)2507 1= 190 y Fd(z)2547 1175 y=0AFh(\))786 b(\(7\))257 1349 y(The)35 b(dihedral)d(a= ngle)h(is)g(p)s=0A(ositiv)m(e,)g(when)h(the)g(p)s(oin)m(t)f Fg(l)43 b Fh(li= es)33=0Ab(on)g(the)h(same)f(side)h(of)f(the)257 1469 y(plane)g(as)f(its)g= =0A(normal)f(v)m(ector,)j(i.e.)43 b(when:)1163 1689 y Ff(~)-46=0Ab(n)1224 1= 704 y Fd(ij)t(k)1319 1722 y Fb(x)1362 1689=0Ay Ff(l)1391 1704 y Fd(x)1457 1= 689 y Fh(+)19 b Ff(~)-46=0Ab(n)1613 1704 y Fd(ij)t(k)1708 1722 y Fb(y)1750 = 1689=0Ay Ff(l)1779 1704 y Fd(y)1843 1689 y Fh(+)19 b Ff(~)-46=0Ab(n)1999 17= 04 y Fd(ij)t(k)2094 1722 y Fb(z)2134 1689=0Ay Ff(l)2163 1704 y Fd(z)2225 16= 89 y Fh(+)22 b Ff(D)30=0Ab(>)e Fh(0)784 b(\(8\))257 1910 y(If)33 b(y)m(ou)h= (go)e(clo)s(c)m=0A(kwise)i(in)e(the)h(Newman)g(pro)5 b(jection,)33 b(the)h(= +0)2568=0A1873 y Fa(\016)2623 1910 y Ff(:)17 b(:)g(:)22 b Fh(+)g(180)3005= =0A1873 y Fa(\016)3077 1910 y Fh(in)m(terv)-5 b(al)32 b(is)257=0A2030 y(on)= h(the)g(righ)m(t,)f(the)h Fe(\000)p Fh(0)1118=0A1994 y Fa(\016)1174 2030 y = Ff(:)17 b(:)g(:)22 b Fe(\000)g=0AFh(180)1557 1994 y Fa(\016)1629 2030 y Fh(= in)m(terv)-5=0Ab(al)31 b(is)h(on)g(the)h(left.)1852 5637 y(2)p eop=0A%%Trai= ler=0Aend=0Auserdict /end-hook known{end-hook}if=0A%%EOF=0A --SUOF0GtieIMvvwua-- From chemistry-request@server.ccl.net Mon Jan 27 00:53:45 2003 Received: from jubilantbiosys.com ([202.144.86.69]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0R5rgP04245 for ; Mon, 27 Jan 2003 00:53:43 -0500 Received: from ramya ( [192.168.1.75] (may be forged)) (authenticated) by jubilantbiosys.com (8.11.6/8.11.6) with ESMTP id h0R5w7e30995 for ; Mon, 27 Jan 2003 11:28:07 +0530 Message-ID: <006f01c2c5c7$f8d026f0$4b01a8c0@jubilant.local> From: "Ramya" To: Subject: CCL: Intramolecular hydrogen bond Date: Mon, 27 Jan 2003 11:20:01 +0530 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_006C_01C2C5F6.083C6E40" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 This is a multi-part message in MIME format. ------=_NextPart_000_006C_01C2C5F6.083C6E40 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hi, How to identify the presence of intramolecular hydrogen bonds in a = given molecule? If someone can help me out with this, it will be great..... Thanks in advance, Ramya ------=_NextPart_000_006C_01C2C5F6.083C6E40 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
Hi,
     How to = identify the=20 presence of intramolecular hydrogen bonds in a given = molecule?
If someone can help me out with this, = it will be=20 great.....
Thanks in advance,
Ramya
------=_NextPart_000_006C_01C2C5F6.083C6E40-- From chemistry-request@server.ccl.net Mon Jan 27 10:21:41 2003 Received: from red.csi.cam.ac.uk ([131.111.8.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0RFLeP30964 for ; Mon, 27 Jan 2003 10:21:40 -0500 Received: from atg21 (helo=localhost) by red.csi.cam.ac.uk with local-esmtp (Exim 4.10) id 18dB4u-0004BC-00 for chemistry@ccl.net; Mon, 27 Jan 2003 15:21:40 +0000 Date: Mon, 27 Jan 2003 15:21:40 +0000 (GMT) From: Alfonso Garcia Sosa X-X-Sender: atg21@red.csi.cam.ac.uk To: chemistry@ccl.net Subject: posphinic acid parameters Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, would anyone have any information/experience on forcefield parameters of phosphinic acid derivatives (a phosporous atom bonded to two oxygens, and to two alifatic carbons which are part of chains): O -C-P-C-O-C- O or | -C- | O=P=O | O | -C- | for use in amber (or other forcefields?). I've had a look in some files and literature but couldn't find the information. There are some old ab-initio studies on their geometries, but no charges, or force constants. Could the data be derived from other data on phosphate or phosphonic data? Specifically, I was looking for P-C, P=O distances and energies; C-P-C, O-P-C, and O-C-P angles; and related dihedrals. Any help would be much appreciated. Thanks and have a nice week -- Alfonso T Garcia-Sosa atg21@cam.ac.uk Tel(44)1223238042, (44)07966465513 http://www.cus.cam.ac.uk/~atg21 Drug Design Group, Dept. of Pharmacology, University of Cambridge & Wolfson College, Cambridge CB3 9BB, UK & De Novo Pharmaceuticals, Histon, Cambridge CB4 9ZR, UK From chemistry-request@server.ccl.net Mon Jan 27 01:22:12 2003 Received: from cascara.uvic.ca ([142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0R6MBP04586 for ; Mon, 27 Jan 2003 01:22:12 -0500 Received: from unix6.uvic.ca (unix6.uvic.ca [142.104.5.87]) by cascara.uvic.ca (8.12.6/8.12.6) with ESMTP id h0R6M9cC206622; Sun, 26 Jan 2003 22:22:10 -0800 Date: Sun, 26 Jan 2003 22:22:09 -0800 (PST) From: Roy Jensen To: chemistry@ccl.net Subject: Re: CCL:How to resolve overlapping Gaussians in the UV Spectrum? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-UVic-Virus-Scanned: OK - Passed virus scan by Sophos (sophie) on cascara X-Scanned-By: MIMEDefang 2.19 (www . roaringpenguin . com / mimedefang) Excel will work, with a little bit of luck... Use the Solver Add-in. Solver can be used to make a non-linear least-squares fitting routine -- which is what you want. It also conveniently plots your results. If you provide me with a fax number, I can fax you some pages out of a lab manual that explain how to do this. Roy Jensen -----BEGIN PGP PUBLIC KEY BLOCK----- Comment: available at www.consol.ca ------END PGP PUBLIC KEY BLOCK------ On Sun, 26 Jan 2003, David J Anick wrote: > Date: Sun, 26 Jan 2003 17:53:24 -0800 > > Dear CCL-ers, > > I have a complex line shape from a spectrum that I would like to > represent as a sum of overlapping Gaussians. More precisely, > I have a function y=f(x), a < x < b, given as about 500 (x,y) > points, where f(a)=f(b)=0, and I would like to find a small > number (typically 3 to 8, perhaps) of Gaussians whose sum > approximates f. I.e. I want to generate parameters {c_i,s_i,b_i} > for which the function > F(x) = SIGMA_i c_i exp(-s_i*(x-b_i)^2) > is a very good approximation to f. > > Can anyone please point me to software, free or not, Linux or > Windows, that can do this? > > Thank you. I will summarize responses. > > David Anick PhD MD > David.Anick@gte.net > (Harvard Medical School) > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Mon Jan 27 15:06:27 2003 Received: from mxout2.cac.washington.edu ([140.142.33.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0RK6RP05549 for ; Mon, 27 Jan 2003 15:06:27 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout2.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.12) with ESMTP id h0RK6HGD015653 for ; Mon, 27 Jan 2003 12:06:17 -0800 Received: from donald ([128.95.128.116]) by smtp.washington.edu (8.12.1+UW01.12/8.12.1+UW02.12) with SMTP id h0RK6Hun018572 for ; Mon, 27 Jan 2003 12:06:17 -0800 Message-ID: <008801c2c63e$72f29e10$74805f80@donald> From: "Carsten Detering" To: Subject: Dock + parallel processing Date: Mon, 27 Jan 2003 20:58:23 +0100 Organization: University of Washington MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Hi all, I am currently trying to compile Dock5 for parallel processing on a dual Xeon RAID5 machine with Redhat linux 8. Does anybody have experience with that?? Here is what I did so far: I changed the bool USE_MPI = false to true in the dock.cpp. Then I compiled the oelib and mpich libraries, as given in the manual. For mpich, everything went fine, only in the oelib, I had an error message; for ./configure, it gave me ./configure line 480 too many arguements ./configure line 483 too many arguements I looked at theses lines and it has to do with the processor type, but I couldnt figure out what the problem is. After typing make, I got another error message: make *** [alchemy.o] error 1. the complation of mpich seems to be fine. And then in the src dir, I followed exactly the instructions in the manual (make -f Makefile.linux clean, dock and install), but for make -f Makefile.linux dock, it gave me make: *** [master_score.lnx.o] Error 1 and for make -f Makefile.linux install, it doesnt find the dock5.linux file which should have been created, but didnt. Anybody got an idea how to solve that?? Apart from that, is it possible to compile Autodock for parallel processing as well? Thanks a lot for any hints/suggestions, Carsten ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Phone 206-543-5081 Fax 206-685-8665 email detering@u.washington.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Mon Jan 27 20:06:45 2003 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0S16jP09406 for ; Mon, 27 Jan 2003 20:06:45 -0500 Received: from cornell.edu (cs666981-224.satx.rr.com [66.69.81.224]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id UAA00327; Mon, 27 Jan 2003 20:06:45 -0500 (EST) Message-ID: <3E35D7CE.F0EED3DC@cornell.edu> Date: Mon, 27 Jan 2003 19:07:27 -0600 From: "Dr. Richard L. Wood" Organization: Cornell University X-Mailer: Mozilla 4.5 [en]C-CCK-MCD {TLC;RETAIL} (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: missing bonds in Rasmol Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all I know I've asked this question before and I received an unsatisfactory answer. I am using the program Rasmol to view xyz coordinate files. Unfortunately, some of the bonds are not being shown. Is there a way that I can click on the two atoms and have a bond appear between them? Alternatively, is there a program (other than WebLab) that is free and runs under windows I can use to display xyz structures and then copy paste them into a Word document? I can copy paste structures from WebLab, but the quality is not good. Thanks, Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Chemistry Trinity University, San Antonio, TX 78212