Re: question about charmm

From: Giulio Vistoli <giulio.vistoli' at \`unimi.it>
Organization: Ist. Chimica Farmaceutica
Subject: Re: question about charmm
Date: Fri, 10 May 2002 10:25:35 +0200
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" <xmao' at \`iris.sipp.ac.cn>
 To: <pdb-l' at \`rcsb.org>
 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
 >
 >
 >
 >
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