From owner-chemistry@ccl.net Sat Dec 19 13:00:01 2009 From: "JOHN MACMILLAN furlip-$-temple.edu" To: CCL Subject: CCL: MacMillan Chemistry preprints in CCL Archives Message-Id: <-40944-091219115833-8057-EjjkVOMaJJhYl8vZB4KiOw%%server.ccl.net> X-Original-From: JOHN MACMILLAN Content-Type: multipart/alternative; boundary=001636e0ba2f4fd5fc047b165035 Date: Sat, 19 Dec 2009 10:14:33 -0500 MIME-Version: 1.0 Sent to CCL by: JOHN MACMILLAN [furlip..temple.edu] --001636e0ba2f4fd5fc047b165035 Content-Type: text/plain; charset=ISO-8859-1 The John H. MacMillan chemistry preprints on the subjects of organic chemistry, polymer chemistry, silanes and silicone chemistry, homogeneous catalysis and precious metal catalysts are now available under the MacMillan directory in the chemistry section of the CCL archives. --001636e0ba2f4fd5fc047b165035 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable The John H. MacMillan chemistry preprints on the subjects of organic chemis= try, polymer chemistry, silanes and silicone chemistry, homogeneous catalys= is and precious metal catalysts are now available under the MacMillan direc= tory in the chemistry section of the CCL archives. --001636e0ba2f4fd5fc047b165035-- From owner-chemistry@ccl.net Sat Dec 19 23:08:00 2009 From: "qiancheng shen qianchengshen|-|gmail.com" To: CCL Subject: CCL: How to know a Nitrogen(or Oxygen) is positively/negatively chagred and a HB acceptor/donor in a PDB formatted(3D) molecule file? Message-Id: <-40945-091219230223-12391-6b+P/mbCMAU+jTA7HBNePg]*[server.ccl.net> X-Original-From: qiancheng shen Content-Type: multipart/alternative; boundary=0016361e7ec0950910047b21095b Date: Sun, 20 Dec 2009 12:02:11 +0800 MIME-Version: 1.0 Sent to CCL by: qiancheng shen [qianchengshen===gmail.com] --0016361e7ec0950910047b21095b Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: quoted-printable Dear CCLers, I got a PDB formatted file(3D, no H added) as following=A3=BA HETATM 1669 C1 BEN A 246 7.788 49.769 56.097 1.00 27.42 C HETATM 1670 C2 BEN A 246 7.885 48.698 56.963 1.00 29.06 C HETATM 1671 C3 BEN A 246 8.055 47.380 56.487 1.00 28.21 C HETATM 1672 C4 BEN A 246 8.244 47.199 55.109 1.00 28.43 C HETATM 1673 C5 BEN A 246 8.213 48.308 54.251 1.00 28.15 C HETATM 1674 C6 BEN A 246 8.009 49.591 54.761 1.00 27.44 C HETATM 1675 C BEN A 246 7.620 51.057 56.597 1.00 27.49 C HETATM 1676 N1 BEN A 246 7.687 51.153 57.930 1.00 28.42 N HETATM 1677 N2 BEN A 246 7.431 52.090 55.801 1.00 24.37 N Anyone know how to calculate the charge of the Nitrogen and how to ensure the Nitrogen is a HB acceptor/donor? Could anyone help me? --0016361e7ec0950910047b21095b Content-Type: text/html; charset=GB2312 Content-Transfer-Encoding: quoted-printable Dear CCLers,
        I got a PDB form= atted file(3D, no H added) as following=A3=BA

   &nbs= p;    HETATM 1669  C1  BEN A 246   =     7.788  49.769  56.097  1.00 27.42 &n= bsp;         C 
 &nbs= p;      HETATM 1670  C2  BEN A 246 =       7.885  48.698  56.963  1.00 2= 9.06           C          HETATM 1671  C3  BEN A= 246       8.055  47.380  56.487&nb= sp; 1.00 28.21           = C 
        HETATM 1672  C4=   BEN A 246       8.244  47.199&nbs= p; 55.109  1.00 28.43        &= nbsp;  C 
        HETATM 1= 673  C5  BEN A 246       8.213 = ; 48.308  54.251  1.00 28.15      &= nbsp;    C 
        HETATM 1674  C6  BEN A= 246       8.009  49.591  54.761&nb= sp; 1.00 27.44           = C 
        HETATM 1675  C&= nbsp;  BEN A 246       7.620  51.05= 7  56.597  1.00 27.49       &n= bsp;   C 
        HET= ATM 1676  N1  BEN A 246       7.687=   51.153  57.930  1.00 28.42     &n= bsp;     N 
        HETATM 1677  N2  BEN A= 246       7.431  52.090  55.801&nb= sp; 1.00 24.37           = N 
 
        Anyone kn= ow how to calculate the charge of the Nitrogen and how to ensure the Nitrog= en is a HB acceptor/donor?
        Co= uld anyone help me?
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