From owner-chemistry@ccl.net Wed Oct 17 07:17:01 2012 From: "quantum chem qchem66-.-gmail.com" To: CCL Subject: CCL: Siesta Message-Id: <-47773-121017071529-8216-MTxAZt+X4LwM6c4pQFPJpA(0)server.ccl.net> X-Original-From: "quantum chem" Date: Wed, 17 Oct 2012 07:15:28 -0400 Sent to CCL by: "quantum chem" [qchem66..gmail.com] Dear members, Please help me in installing and working with SIESTA package on ubuntu.I need to carry out some calculations on atomic clusters. thanks qc From owner-chemistry@ccl.net Wed Oct 17 08:37:00 2012 From: "Artem R. Oganov artem.oganov---sunysb.edu" To: CCL Subject: CCL: Workshop "Crystal Structure Prediction with USPEX Code" (10-15 Dec'12) Message-Id: <-47774-121017025816-21837-9iQ6bxCvAiUmby904AEr1w%%server.ccl.net> X-Original-From: "Artem R. Oganov" Date: Wed, 17 Oct 2012 02:58:15 -0400 Sent to CCL by: "Artem R. Oganov" [artem.oganov(_)sunysb.edu] Dear colleagues and friends, We are happy to announce the upcoming hands-on workshop on crystal structure prediction using the USPEX code in Stony Brook on December 10-15, 2012. The workshop registration fee is $500 and this covers hotel accommodation during the whole workshop and most meals, banquet at the University President's residence, and an excursion on Long Island. Registration is open until November 9 (November 16 for late registration). We could get such low all-covering rates thanks to generous funding. USPEX is the most widely used tool in the world for crystal structure prediction, with over 1000 users. Theory lectures and practical hands-on sessions will be given by its developers and users, and some of the world's leading international experts in related fields. The program and further information can be found here: http://han.ess.sunysb.edu/~aoganov/Workshop_US.html For registration, click here: http://naples.cc.sunysb.edu/secct/sbfevents.nsf/uspex The workshop is funded by the NSF, COMPRES, and by Stony Brook University. Its organization is handled by Stony Brook University's Conference Organization team. From owner-chemistry@ccl.net Wed Oct 17 09:12:00 2012 From: "Mannan K malie_03]|[yahoo.co.in" To: CCL Subject: CCL: Stability of D-aminoacid in an alphahelix Message-Id: <-47775-121017031226-22296-+tXcGZKh7cLp/NhuYTQEPQ:server.ccl.net> X-Original-From: "Mannan K" Date: Wed, 17 Oct 2012 03:12:24 -0400 Sent to CCL by: "Mannan K" [malie_03||yahoo.co.in] I have a peptide with 12 residues with L-amino acid of which, the 6th residue is a D-aminoacid. We got this peptide from a company which is known for making such things. We performed few wet-lab experiments using this peptide and also compared the results with the peptide of L-aminoacids only. The only difference between these two peptides (12-mer), we have either D-aminoacid or L-aminoacid in the 6th position. But the question, what would be the stability of this D-aminoacid in a middle of L-aminoacids, will it flip back to L-aminoacid? or will it create any strain with other L-aminoacid residues. From owner-chemistry@ccl.net Wed Oct 17 09:46:00 2012 From: "Reaz Uddin riaasuddin[]yahoo.com" To: CCL Subject: CCL: Help required for .sdf file IDs (AWK) Message-Id: <-47776-121017092444-31854-OFAb50uxbyzldyYAvZsZ6g/a\server.ccl.net> X-Original-From: Reaz Uddin Content-Type: multipart/alternative; boundary="-1049307544-218887320-1350480269=:57817" Date: Wed, 17 Oct 2012 06:24:29 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Reaz Uddin [riaasuddin]=[yahoo.com] ---1049307544-218887320-1350480269=:57817 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello folks, I've posted content of sdf file below. I'd appreciate if someone can help m= e to move the IDs of each compound up, before this " -ABC- 1D " . For example=A0 0001=A0 [after line "> (0001) "] should print before "= -ABC- 1D ". I'd prefer help using awk script. Thank you so much. With best wishes=20 Reaz -ABC- 1D 30 34 0 0 0 0 0 0 0 0999 V2000 -0.1958 -3.1167 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 2.7292 -4.0875 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.1958 -1.4625 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -0.9083 -1.8667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2250 -4.7542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1958 -3.9417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9500 -4.3500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7417 -5.4250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5167 -4.3500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9083 -2.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9542 -5.1750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5167 -1.8667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2292 -3.9375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5167 -2.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6250 -1.4500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9083 -4.3542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1958 -0.6292 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.5167 -5.1792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2292 -5.5917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0500 -4.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4625 -4.0250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4500 -0.1167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8750 -0.1750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0542 -3.3042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2875 -4.0292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6583 0.6208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1542 0.6583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7042 -3.3167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4667 -2.5917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3000 -2.6000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 7 1 0 0 0 0 3 12 1 0 0 0 0 4 10 1 0 0 0 0 5 2 2 0 0 0 0 6 1 1 0 0 0 0 7 13 2 0 0 0 0 8 11 1 0 0 0 0 9 6 1 0 0 0 0 10 1 1 0 0 0 0 11 19 2 0 0 0 0 12 14 1 0 0 0 0 13 9 1 0 0 0 0 14 1 1 0 0 0 0 15 4 2 0 0 0 0 16 6 2 0 0 0 0 17 3 1 0 0 0 0 18 9 2 0 0 0 0 19 18 1 0 0 0 0 20 5 1 0 0 0 0 21 20 1 0 0 0 0 22 17 1 0 0 0 0 23 17 1 0 0 0 0 24 21 2 0 0 0 0 25 21 1 0 0 0 0 26 23 1 0 0 0 0 27 22 1 0 0 0 0 28 25 2 0 0 0 0 29 24 1 0 0 0 0 30 28 1 0 0 0 0 4 3 1 0 0 0 0 7 11 1 0 0 0 0 26 27 1 0 0 0 0 8 5 1 0 0 0 0 29 30 2 0 0 0 0 M END > (0001) 0001 $$$$ -ABC- 1D 32 34 0 0 0 0 0 0 0 0999 V2000 3.9042 -8.8292 0.0000 S 0 0 3 0 0 0 0 0 0 0 0 0 5.3375 -6.3542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3250 -7.1750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8417 -7.8417 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.0542 -6.7667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8417 -6.5125 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 5.3292 -5.5250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0542 -7.5917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4292 -5.4292 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.1917 -5.1125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1167 -4.2917 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 3.9042 -8.0042 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.6042 -5.1167 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.6250 -7.5917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3375 -8.0042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9042 -9.6542 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 1.8917 -4.8125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6250 -6.7667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3167 -4.1042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9000 -5.5417 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 4.7375 -8.8292 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0792 -8.8292 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.1500 -7.1750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0375 -5.1042 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.0917 -5.7250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5667 -7.8917 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.1875 -10.0667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6250 -10.0750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0667 -4.8875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8917 -6.3667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3917 -7.8875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1542 -8.6042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 18 1 0 0 0 0 3 4 2 0 0 0 0 4 8 1 0 0 0 0 5 2 2 0 0 0 0 6 5 1 0 0 0 0 7 2 1 0 0 0 0 8 15 2 0 0 0 0 9 10 2 0 0 0 0 10 20 1 0 0 0 0 11 10 1 0 0 0 0 12 1 1 0 0 0 0 13 7 1 0 0 0 0 14 12 1 0 0 0 0 15 14 1 0 0 0 0 16 1 1 0 0 0 0 17 9 1 0 0 0 0 18 14 2 0 0 0 0 19 11 1 0 0 0 0 20 13 1 0 0 0 0 21 1 2 0 0 0 0 22 1 2 0 0 0 0 23 3 1 0 0 0 0 24 7 2 0 0 0 0 25 6 1 0 0 0 0 26 23 1 0 0 0 0 27 16 1 0 0 0 0 28 16 1 0 0 0 0 29 17 1 0 0 0 0 30 20 1 0 0 0 0 31 26 1 0 0 0 0 32 26 1 0 0 0 0 5 8 1 0 0 0 0 6 3 1 0 0 0 0 17 19 2 0 0 0 0 M END > (0008) 0008 $$$$ -ABC- 1D 29 32 0 0 0 0 0 0 0 0999 V2000 7.3167 -7.0542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8417 -6.3792 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 7.0625 -7.8417 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.4750 -7.8417 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.8792 -8.4125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.1542 -8.0167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3042 -7.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6125 -8.4542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1292 -7.0917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3292 -5.7167 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 8.1042 -6.8042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3542 -6.3667 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 6.0167 -6.3667 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 8.1042 -5.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6000 -7.0875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6000 -5.6542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5292 -6.3667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3625 -9.2417 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.4292 -8.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7750 -5.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7750 -7.0792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4042 -8.3750 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 8.6792 -7.4917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9792 -8.8792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7167 -7.9042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3417 -9.1917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7917 -8.7042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4792 -7.3125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0417 -7.9167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 0 0 0 0 3 1 1 0 0 0 0 4 9 2 0 0 0 0 5 4 1 0 0 0 0 6 7 2 0 0 0 0 7 9 1 0 0 0 0 8 3 1 0 0 0 0 9 17 1 0 0 0 0 10 2 1 0 0 0 0 11 1 2 0 0 0 0 12 20 1 0 0 0 0 13 2 1 0 0 0 0 14 11 1 0 0 0 0 15 13 1 0 0 0 0 16 13 1 0 0 0 0 17 12 1 0 0 0 0 18 8 2 0 0 0 0 19 8 1 0 0 0 0 20 16 1 0 0 0 0 21 15 1 0 0 0 0 22 6 1 0 0 0 0 23 19 2 0 0 0 0 24 19 1 0 0 0 0 25 22 1 0 0 0 0 26 22 1 0 0 0 0 27 24 2 0 0 0 0 28 23 1 0 0 0 0 29 27 1 0 0 0 0 10 14 2 0 0 0 0 21 12 1 0 0 0 0 29 28 2 0 0 0 0 5 6 1 0 0 0 0 M END > (0002) 0002 $$$$ ---1049307544-218887320-1350480269=:57817 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Hello folks,
I= 've posted content of sdf file below. I'd appreciate if someone can help me= to move the
I= Ds of each compound up, bef= ore this "= -ABC- 1D " .
For example  0001  [after line "> <ID> (0001) "] should prin= t before <= span style=3D"font-family: tahoma,new york,times,serif;">" -ABC- 1D ".
= I'd prefer help using awk script.
Thank you so much.
With best wishes
Reaz
<= /span>

  -ABC-  1D
 30 34  0  0  0  0  0  0  0  0999 V2000
   -0.1958   -3.1167    0.0000 =
N   0  0  3  0  0  0  0  0  0  0  0  0
    2.7292   -4.0875    0.0000 N =
  0  0  0  0  0  0  0  0  0  0  0  0
   -0.1958   -1.4625    0.0000 N   =
0  0  3  0  0  0  0  0  0  0  0  0
   -0.9083   -1.8667    0.0000 C   0 =
 0  0  0  0  0  0  0  0  0  0  0
    3.2250   -4.7542    0.0000 C   0  0=
  0  0  0  0  0  0  0  0  0  0
   -0.1958   -3.9417    0.0000 C   0  0  =
0  0  0  0  0  0  0  0  0  0
    1.9500   -4.3500    0.0000 C   0  0  0 =
 0  0  0  0  0  0  0  0  0
    2.7417   -5.4250    0.0000 O   0  0  0  0=
  0  0  0  0  0  0  0  0
    0.5167   -4.3500    0.0000 C   0  0  0  0  =
0  0  0  0  0  0  0  0
   -0.9083   -2.7000    0.0000 C   0  0  0  0=20
 0  0  0  0  0  0  0  0
    1.9542   -5.1750    0.0000 C   0  0  0  0  0=
  0  0  0  0  0  0  0
    0.5167   -1.8667    0.0000 C   0  0  0  0  0  =
0  0  0  0  0  0  0
    1.2292   -3.9375    0.0000 C   0  0  0  0  0  0 =
 0  0  0  0  0  0
    0.5167   -2.7000    0.0000 C   0  0  0  0  0  0  0=
  0  0  0  0  0
   -1.6250   -1.4500    0.0000 O   0  0  0  0  0  0  0  =
0  0  0  0  0
   -0.9083   -4.3542    0.0000 O   0  0  0  0  0  0  0  0 =
 0  0  0  0
   -0.1958   -0.6292    0.0000 C   0  0  3  0  0  0  0  0  0=
  0  0  0
    0.5167   -5.1792    0.0000 C   0  0  0  0  0  0  0  0  0  =
0  0  0
    1.2292   -5.5917    0.0000 C   0  0  0  0  0  0  0  0  0  0 =
 0  0
    4.0500   -4.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0=
  0
    4.4625   -4.0250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  =
0
    0.4500   -0.1167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0<=
br>   -0.8750   -0.1750    0.0000 C   0  0  0  0  0  0  0  0  0  0=20
 0  0
    4.0542   -3.3042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0=
  0
    5.2875   -4.0292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  =
0
   -0.6583    0.6208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0<=
br>    0.1542    0.6583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    5.7042   -3.3167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 =
   4.4667   -2.5917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   =
 5.3000   -2.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  =
7  1  0  0  0  0
  3 12  1  0  0  0  0
  4 10  1  0  0  0  0
  5  =
2  2  0  0  0  0
  6  1  1  0  0  0  0
  7 13  2  0  0  0  0
  8 1=
1  1  0  0  0  0
  9  6  1  0  0  0  0
 10  1  1  0  0  0  0
 11 1=
9  2  0  0  0  0
 12 14  1  0  0  0  0
 13  9  1  0  0  0  0
 14  =
1  1  0  0  0  0
 15  4  2  0  0  0  0
 16  6  2  0  0  0  0
 17  =
3  1  0  0  0  0
 18  9  2  0  0  0  0
 19 18  1  0  0  0=20
 0
 20  5  1  0  0  0  0
 21 20  1  0  0  0  0
 22 17  1  0  0  0 =
 0
 23 17  1  0  0  0  0
 24 21  2  0  0  0  0
 25 21  1  0  0  0 =
 0
 26 23  1  0  0  0  0
 27 22  1  0  0  0  0
 28 25  2  0  0  0 =
 0
 29 24  1  0  0  0  0
 30 28  1  0  0  0  0
  4  3  1  0  0  0 =
 0
  7 11  1  0  0  0  0
 26 27  1  0  0  0  0
  8  5  1  0  0  0 =
 0
 29 30  2  0  0  0  0
M  END
>  <ID> (0001)
0001
$$$$

  -ABC-  1D

 32 34  0  0  0  0  0  0  0  0999 V2000=

    3.9042   -8.8292    0.0000 S   0  0  3  0  0  0  0  0  0  0  0  0    5.3375   -6.3542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
=
    7.3250   -7.1750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  =
  6.8417   -7.8417    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    =
6.0542   -6.7667    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.=
8417   -6.5125    0.0000 N   0  0  3  0  0  0  0  0  0  0  0  0
=20
   5.3292   -5.5250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   =
 6.0542   -7.5917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2=
.4292   -5.4292    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1=
917   -5.1125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.116=
7   -4.2917    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.9042 =
  -8.0042    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6042   =
-5.1167    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6250   -7=
.5917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3375   -8.0=
042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9042   -9.654=
2    0.0000 N   0  0  3  0  0  0  0  0  0  0  0  0
    1.8917   -4.8125 =
   0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6250   -6.7667   =
 0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3167   -4.1042    0=
.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9000   -5.5417
    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
    4.7375   -8.8292  =
  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0792   -8.8292    =
0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1500   -7.1750    0.=
0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0375   -5.1042    0.00=
00 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0917   -5.7250    0.0000=
 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5667   -7.8917    0.0000 C=
   0  0  3  0  0  0  0  0  0  0  0  0
    3.1875  -10.0667    0.0000 C  =
 0  0  0  0  0  0  0  0  0  0  0  0
    4.6250  -10.0750    0.0000 C   0=
  0  0  0  0  0  0  0  0  0  0  0
    1.0667   -4.8875    0.0000 C   0  =
0  0  0  0  0  0  0  0  0  0  0
    3.8917   -6.3667    0.0000 C   0  0 =
 0  0  0  0  0  0  0  0  0  0
    9.3917   -7.8875    0.0000 C   0  0  0=
  0  0  0  0  0  0  0  0  0
    8.1542   -8.6042    0.0000 C   0  0  0  =
0  0  0  0  0  0  0  0  0
  2 18  1  0  0  0  0
  3  4  2  0=20
 0  0  0
  4  8  1  0  0  0  0
  5  2  2  0  0  0  0
  6  5  1  0 =
 0  0  0
  7  2  1  0  0  0  0
  8 15  2  0  0  0  0
  9 10  2  0 =
 0  0  0
 10 20  1  0  0  0  0
 11 10  1  0  0  0  0
 12  1  1  0 =
 0  0  0
 13  7  1  0  0  0  0
 14 12  1  0  0  0  0
 15 14  1  0 =
 0  0  0
 16  1  1  0  0  0  0
 17  9  1  0  0  0  0
 18 14  2  0 =
 0  0  0
 19 11  1  0  0  0  0
 20 13  1  0  0  0  0
 21  1  2  0 =
 0  0  0
 22  1  2  0  0  0  0
 23  3  1  0  0  0  0
 24  7  2  0 =
 0  0  0
 25  6  1  0  0  0  0
 26 23  1  0  0  0  0
 27 16  1  0 =
 0  0  0
 28 16  1  0  0  0  0
 29 17  1  0  0  0  0
 30 20  1  0 =
 0  0  0
 31 26  1  0  0  0  0
 32 26  1  0  0  0  0
  5  8  1  0 =
 0  0  0
  6  3  1  0  0  0  0
 17 19  2  0  0  0  0
M  END
>=
;  <ID> (0008)
0008

$$$$

  -ABC-  1D

 29 32  =
0  0  0  0  0  0  0  0999 V2000
    7.3167   -7.0542    0.0000 C=20
  0  0  0  0  0  0  0  0  0  0  0  0
    6.8417   -6.3792    0.0000 N   =
0  0  3  0  0  0  0  0  0  0  0  0
    7.0625   -7.8417    0.0000 N   0 =
 0  0  0  0  0  0  0  0  0  0  0
    3.4750   -7.8417    0.0000 N   0  0=
  0  0  0  0  0  0  0  0  0  0
    2.8792   -8.4125    0.0000 N   0  0  =
0  0  0  0  0  0  0  0  0  0
    2.1542   -8.0167    0.0000 C   0  0  0 =
 0  0  0  0  0  0  0  0  0
    2.3042   -7.2000    0.0000 C   0  0  0  0=
  0  0  0  0  0  0  0  0
    7.6125   -8.4542    0.0000 C   0  0  0  0  =
0  0  0  0  0  0  0  0
    3.1292   -7.0917    0.0000 C   0  0  0  0  0 =
 0  0  0  0  0  0  0
    7.3292   -5.7167    0.0000 N   0  0  0  0  0  0=
  0  0  0  0  0  0
    8.1042   -6.8042    0.0000 C   0  0  0  0  0  0  =
0  0  0  0  0  0
    4.3542   -6.3667    0.0000 N   0  0  3  0  0  0  0 =
 0  0  0  0  0
    6.0167   -6.3667    0.0000 C   0  0  3  0  0  0  0  0=
  0  0  0  0
    8.1042   -5.9750    0.0000 C   0  0  0  0  0  0=20
 0  0  0  0  0  0
    5.6000   -7.0875    0.0000 C   0  0  0  0  0  0  0=
  0  0  0  0  0
    5.6000   -5.6542    0.0000 C   0  0  0  0  0  0  0  =
0  0  0  0  0
    3.5292   -6.3667    0.0000 C   0  0  0  0  0  0  0  0 =
 0  0  0  0
    7.3625   -9.2417    0.0000 O   0  0  0  0  0  0  0  0  0=
  0  0  0
    8.4292   -8.2750    0.0000 C   0  0  0  0  0  0  0  0  0  =
0  0  0
    4.7750   -5.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0 =
 0  0
    4.7750   -7.0792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0=
  0
    1.4042   -8.3750    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  =
0
    8.6792   -7.4917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0<=
br>    8.9792   -8.8792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    0.7167   -7.9042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 =
   1.3417   -9.1917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   =
 9.7917   -8.7042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0=20
 0
    9.4792   -7.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0=

   10.0417   -7.9167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  9  2  0  0  0  0  5  4  1  0  0  0  0
  6  7  2  0  0  0  0
  7  9  1  0  0  0  0  8  3  1  0  0  0  0
  9 17  1  0  0  0  0
 10  2  1  0  0  0  0 11  1  2  0  0  0  0
 12 20  1  0  0  0  0
 13  2  1  0  0  0  0 14 11  1  0  0  0  0
 15 13  1  0  0  0  0
 16 13  1  0  0  0  0 17 12  1  0  0  0  0
 18  8  2  0  0  0  0
 19  8  1  0  0  0  0 20 16  1  0  0  0  0
 21 15  1  0  0  0  0
 22  6  1  0  0  0  0 23 19  2  0  0  0  0
 24 19  1  0  0  0  0
 25 22  1  0  0  0  0 26 22  1  0  0  0  0
 27 24  2  0  0  0  0
 28 23  1  0  0  0  0 29 27  1  0  0  0  0
 10 14  2  0  0  0  0
 21 12  1  0  0  0  0 29 28  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
>=20
 <ID> (0002)
0002

$$$$
---1049307544-218887320-1350480269=:57817-- From owner-chemistry@ccl.net Wed Oct 17 11:07:00 2012 From: "Wolf Ihlenfeldt wdi() xemistry.com" To: CCL Subject: CCL: Help required for .sdf file IDs (AWK) Message-Id: <-47777-121017105808-2735-mVdzHxEF0xRHnicjWLJjSg|*|server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=14dae9cdc76533512204cc427f2b Date: Wed, 17 Oct 2012 16:58:00 +0200 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi*|*xemistry.com] --14dae9cdc76533512204cc427f2b Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Reaz, a) The posted file excerpt is unusable. In SD files, spaces are significant, and they got lost here, at least in Google mail. b) What exactly do you mean by 'before'? If you mean on the 2nd line of each record, as a prefix: That is impossible without breaking the file syntax. There is not enough room in that field. c) If you want it in the first line of a record, here is a script for the Cactvs Chemoinformatics Toolkit (free academic versions at www.xemistry.com/academic): --snip-- set fh [molfile open stdout w] molfile loop [lindex $argv 0] eh { ens set $eh E_MDL_NAME [ens get $eh ID] molfile write $fh $eh } --snip-- Run as 'csts -f scriptfile my_sd_file >my_fixed_sd_file' d) Using any simple file line processing tool such as awk, python, sed, etc. to process SD files is a really bad idea. There is no way to reliably determine record boundaries without understanding the file syntax. '$$$$' is legal data in various places. e) For an overview about other toolkits which could help you with this task, visit http://ctr.wikia.com/wiki/Chemistry_Toolkit_Rosetta_Wiki On Wed, Oct 17, 2012 at 3:24 PM, Reaz Uddin riaasuddin[]yahoo.com < owner-chemistry[-]ccl.net> wrote: > > Hello folks, > I've posted content of sdf file below. I'd appreciate if someone can help > me to move the > IDs of each compound up, before this " -ABC- 1D " . > For example 0001 [after line "> (0001) "] should print before " > -ABC- 1D ". > I'd prefer help using awk script. > Thank you so much. > With best wishes > Reaz > > --=20 Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi[-]xemistry.com Phone: +49 6174 201455 - Fax +49 6174 209665 --- xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr. W.= D. Ihlenfeldt Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany HR K=C3=B6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 --14dae9cdc76533512204cc427f2b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Reaz,

a) The posted file excerpt is unusable. In SD files, sp= aces are significant, and they got lost here, at least in Google mail.
<= br>b) What exactly do you mean by 'before'? If you mean on the 2nd = line of each record, as a prefix: That is impossible without breaking the f= ile syntax. There is not enough room in that field.

c) If you want it in the first line of a record, here is a script for t= he Cactvs Chemoinformatics Toolkit (free academic versions at www.xemistry.com/academic):

--sn= ip--
set fh [molfile open stdout w]
molfile loop [lindex $argv 0] eh {
=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 ens set $eh E_MDL_NAME [ens get $eh= ID]
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 molfile write $fh $eh}
--snip--

Run as 'csts -f scriptfile my_sd_file >my_fixe= d_sd_file'

d) Using any simple file line processing tool such as awk, python, sed,= etc. to process SD files is a really bad idea. There is no way to reliably= determine record boundaries without understanding the file syntax. '$$= $$' is legal data in various places.

e) For an overview about other toolkits which could help you with this = task, visit http://ctr.wikia.com/wiki/Chemistry_Toolkit_Rosetta_Wiki




On Wed, Oct 17, 2012 at 3:24 PM, Rea= z Uddin riaasuddin[]yahoo.com <owne= r-chemistry[-]ccl.net> wrote:

Hello folks,
I've posted content of sdf file below. I'd apprecia= te if someone can help me to move the
IDs of each compound up, before this " -ABC- 1D " .
For example=C2=A0 0001=C2=A0 [after line "> <ID> (0001) "] should print before " -ABC- 1D ".
I'd prefer help using awk script.
Thank you so much.
With best wishes
Reaz
<= /span>


--
Wolf-D. Ihlenfeldt -=C2=A0 Xemistry GmbH - wdi[-]xemistry.com
Phone: +49 6174 201455 - Fax +49 6174 209665
---
xemistry gmbh =E2=80= =93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr. W. D. Ihlenfeldt
Ad= dress: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany
HR K=C3=B6nigste= in B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719

--14dae9cdc76533512204cc427f2b-- From owner-chemistry@ccl.net Wed Oct 17 12:50:00 2012 From: "=?UTF-8?Q?Gunda_Tam=C3=A1s?= gunda.tamas%a%pharm.unideb.hu" To: CCL Subject: CCL: Stability of D-aminoacid in an alphahelix Message-Id: <-47778-121017122811-20590-IzrrMKdTDfXTv5SN35uc8A_._server.ccl.net> X-Original-From: =?UTF-8?Q?Gunda_Tam=C3=A1s?= Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 17 Oct 2012 18:28:02 +0200 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Gunda_Tam=C3=A1s?= [gunda.tamas- -pharm.unideb.hu] Under normal physiological conditions the D-amino acid is stable, it will not change its configuration. Extreme conditions would be necessary to equilibrate the amino acid (and in this case the L-amino acids would change their configuration or the peptide would decompose as well). As to the second question, molecular modelling would be necessary to tell the changes in the conformation of the peptide. Best regards Tamas Gunda On Wed, 17 Oct 2012 03:12:24 -0400, Mannan K malie_03]|[yahoo.co.in wrote: > Sent to CCL by: "Mannan K" [malie_03||yahoo.co.in] > I have a peptide with 12 residues with L-amino acid of which, the 6th > residue is a D-aminoacid. > > We got this peptide from a company which is known for making such > things. > We performed few wet-lab experiments using this peptide and also > compared the results with the peptide of L-aminoacids only. > > The only difference between these two peptides (12-mer), we have > either D-aminoacid or L-aminoacid in the 6th position. > > But the question, > what would be the stability of this D-aminoacid in a middle of > L-aminoacids, will it flip back to L-aminoacid? > or > will it create any strain with other L-aminoacid residues. > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ From owner-chemistry@ccl.net Wed Oct 17 15:23:00 2012 From: "Venable, Richard (NIH/NHLBI) E venabler(!)nhlbi.nih.gov" To: CCL Subject: CCL: Stability of D-aminoacid in an alphahelix Message-Id: <-47779-121017133850-4559-CuOMJrITgMUQRzwiR7FhKA,,server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 17 Oct 2012 13:37:28 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler]~[nhlbi.nih.gov] It should be noted that chiral inversion can occur in modeling with force fields, esp. with various accelerated sampling methods which raise the temperature or lower barriers, such as replica exchange or self-guided methods, respectively. -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 10/17/12 12:28 PM, "Gunda Tamás gunda.tamas%a%pharm.unideb.hu" wrote: >Sent to CCL by: =?UTF-8?Q?Gunda_Tam=C3=A1s?= [gunda.tamas- >-pharm.unideb.hu] > Under normal physiological conditions the D-amino acid is stable, it > will not change its configuration. Extreme conditions would be necessary > to equilibrate the amino acid (and in this case the L-amino acids would > change their configuration or the peptide would decompose as well). > > As to the second question, molecular modelling would be necessary to > tell the changes in the conformation of the peptide. > > Best regards > > Tamas Gunda > On Wed, 17 Oct 2012 03:12:24 -0400, Mannan K malie_03]|[yahoo.co.in > wrote: >> Sent to CCL by: "Mannan K" [malie_03||yahoo.co.in] >> I have a peptide with 12 residues with L-amino acid of which, the 6th >> residue is a D-aminoacid. >> >> We got this peptide from a company which is known for making such >> things. >> We performed few wet-lab experiments using this peptide and also >> compared the results with the peptide of L-aminoacids only. >> >> The only difference between these two peptides (12-mer), we have >> either D-aminoacid or L-aminoacid in the 6th position. >> >> But the question, >> what would be the stability of this D-aminoacid in a middle of >> L-aminoacids, will it flip back to L-aminoacid? >> or >> will it create any strain with other L-aminoacid residues. From owner-chemistry@ccl.net Wed Oct 17 22:05:00 2012 From: "Hanneke Jansen johanna.jansen|a|novartis.com" To: CCL Subject: CCL: Winners from first TDT competition have been selected! Message-Id: <-47780-121017204758-11541-zx+w+ZUe5URv62Rqd1oWAg!A!server.ccl.net> X-Original-From: "Hanneke Jansen" Date: Wed, 17 Oct 2012 20:47:54 -0400 Sent to CCL by: "Hanneke Jansen" [johanna.jansen[-]novartis.com] Dear Colleagues, The TDT Steering Committee is excited to announce the results of the first TDT competition. We received a total of six tutorials in four categories and all six were rated on a scale of 1-10 for these criteria: Scientific content, Presentation & Clarity, Educational benefit, and Reproducibility. From the six submissions, an overall winner and three runners-up were selected based on the combined score from all criteria. These winners are: Overall winner, addressing challenge 2 3D-QSAR-boosted SBVS Paolo Tosco Department of Drug Science and Technology, Torino (Italy) First runner-up, addressing challenge 2 Teaching molecular interactions with online interactive pharmacophore modeling David Ryan Koes and Carlos J. Camacho Department of Computational and Systems Biology, University of Pittsburgh Second runner-up, addressing challenge 4 Public domain chemical databases for malaria drug discovery George Nicola, Tiqing Liu, Michael Gilson University of California, San Diego Third runner-up, addressing challenge 3 Structure-based drug design for trypanosomal PDEB1 Khaled M. Elokely, Robert J. Doerksen University of Mississippi School of Pharmacy All four winners will be recognized at the Award Symposium at the next ACS National Meeting (April 7-11, New Orleans) where they will have an opportunity to present their work. All materials submitted to the competition will be made available through the TDT website at the time of the Award Symposium. We thank all of the submitters for their contributions and efforts. We also thank the judging panel for thoughtful and detailed analyses: Pat Walters (Chair, Vertex), Yvonne Martin (Abbott, retired), Steve Johnson (BMS), Rajarshi Guha (NIH/NCATS), Steve Dixon (Schrdinger). Financial sponsorship for the Travel Awards given to the four winners is gratefully acknowledged from the following organizations: ACS Innovative Projects Grant, Knime, OpenEye, and Cresset. We hope to see you at the Award symposium! The TDT Steering Committee Hanneke Jansen, Rommie Amaro, Jane Tseng and Wendy Cornell