From chemistry-request {*at*} server.ccl.net Fri May 10 04:25:58 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4A8PwU24488 for ; Fri, 10 May 2002 04:25:58 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0GVV00AGGZE1WO-: at :-mailstudenti.unimi.it> for chemistry-: at :-ccl.net; Fri, 10 May 2002 10:25:14 +0200 (MEST) Received: from vega (vega.farma.unimi.it [159.149.79.32]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0GVV008AMZE301 _-at-_)smtp.unimi.it> for chemistry _-at-_)ccl.net; Fri, 10 May 2002 10:25:15 +0200 (MEST) Date: Fri, 10 May 2002 10:25:35 +0200 From: Giulio Vistoli Subject: Re: question about charmm To: Mao Xiang , CCL Message-id: <004701c1f7fc$4253ec20$204f959f ":at:" farma.unimi.it.farma.unimi.it> Organization: Ist. Chimica Farmaceutica MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Content-type: text/plain; charset=gb2312 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal References: <3CD9BBF2.1379B8F4 {*at*} iris.sipp.ac.cn> Dear Mao Xiang Vega is able to solvate any molecule with any solvent and can save it in several formats Try it (http://users.unimi.it/~ddl) Best regards Giulio Vistoli -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39 02 503 17522 Fax +39 02 503 17565 E-Mail: giulio.vistoli- at -unimi.it WWW: http://users.unimi.it/~ddl ----- Original Message ----- From: "Mao Xiang" To: Sent: Thursday, May 09, 2002 1:59 AM Subject: question about charmm > pdb-l > > Hello everyone: > Here is some questions that I need your help. I wonder if > anyone could tell me how to generate any size of water sphere using > charmm. And When I generated a large box(90A), and want to cut it to the > sphere, Charmm would not read in the coordinate file, I think it is > because it could not differ the first and the second coloum in the > coordinate like the following: > > ----------------------------- > 8099126997 TIP3 H2 -42.02900 -42.78300 -32.56100 ABC 997 0.00000 > 8099226998 TIP3 OH2 -17.48700 -32.81400 -42.10200 ABC 998 0.00000 > 8099326998 TIP3 H1 -17.43100 -32.94900 -41.15600 ABC 998 0.00000 > 8099426998 TIP3 H2 -18.18400 -33.40500 -42.38800 ABC 998 0.00000 > 8099526999 TIP3 OH2 -28.39600 -45.51900 -16.52900 ABC 999 0.00000 > 8099626999 TIP3 H1 -28.88800 -46.30300 -16.28500 ABC 999 0.00000 > 8099726999 TIP3 H2 -27.63500 -45.85300 -17.00500 ABC 999 0.00000 > 8099827000 TIP3 OH2 -37.27900 -37.63700 -39.21200 ABC 1000 0.00000 > 8099927000 TIP3 H1 -37.93700 -37.80100 -38.53500 ABC 1000 0.00000 > 8100027000 TIP3 H2 -37.51000 -38.24000 -39.91900 ABC 1000 0.00000 > ----------------------------- > So I wonder if you have some good ways to generate large water sphere, > for example 50A in the radius. > > Another question is how to generate the TIP3P deformable boundary force > for a water sphere . > > Thanks in advance. > > > Regards, > mao xiang > > > > > *** Details on how to be removed from this list as well as an *** > *** archive of recent postings are available at *** > *** http://www.rcsb.org/pdb/forum.html *** >