Re: CCL:basis set optimiser in solid

[xin_hu <xxh0541 { *at * } hotmail.com>]

Hello:
 I am a newer of AMBER6.0 and just try to learn how to use it. Maybe it is a
 stupid question but hopefully someone give me a help. My questions are 1) Can I
 load a pdb file of protein,  assign the residues with charges, and save the file
 as pdb or other type formate? if can, what's kind of charge it is assigned?  2)
 How to just add polar hydrogen (united atom) to residues, and how to assign the
 kollman united atom charges using AMBER6.0?
 I appreciate your help. Thanks.
 xin hu
 Dept of Pharmacy
 NDSU
 Samantha Jenkins wrote:
 > Sergei Tretiak wrote:
 > >
 > > Kevin,
 > >
 > > MOLDEN (http://www.cmbi.kun.nl/~schaft/molden/molden.html) will do
 the
 > > job for you. It can generate graphics GIF files for each step and play
 it
 > > like a movie, but to merge all GIFs into a single movie file you have
 to
 > > use another software.
 > >
 > > Best,
 > >
 > > Sergei
 > >
 > >
 >.-----------------------------------------------------------------------.
 > > |\  / \ |               Sergei Tretiak                          | / \
 /|
 > >
 |.\/...\|.......................................................|/...\/.|
 > > | Theoretical Division        | Voice: (505) 667-8351
 |
 > > | Mail stop B262              | Fax:   (505) 665-4063
 |
 > > | Los Alamos National Lab     | E-mail: serg { *at * }
 markov.chem.rochester.edu  |
 > > | Los Alamos, NM 87545        |         serg { *at * }
 wigner.chem.rochester.edu  |
 > > |    Homepage: http://markov.chem.rochester.edu/serg/welcome.html       |
 > >
 |_______________________________________________________________________|
 > Hello.
 >
 > I am trying to optimise basis sets using LOPTCG within crytsal98 and I
 > am having little success. Does anyone have a working set of input files
 > for LOPTCG, which optimse the basis set. The code seem to work OK for
 > geometries and comes with example files for the geometries, but not the
 > basis sets.
 > Any simple solid would do, diamond etc.
 >
 > Thanks,
 >
 > Samantha Jenkins
 >
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 --
 *************************************************
    Xin Hu
    Department of Pharmaceutical Science
    College of Pharmacy
    North Dakota State University
    Fargo, ND 58105
    Tel: 701-231-8298 (O)
          701-231-4360 (H)
    Fax: 701-231-7781
    E-mail: Xin_Hu { *at * } ndsu.nodak.edu
               xxh0541 { *at * } hotmail.com
 *************************************************