[gmx-users] Re: How to use the dummy atom?
spoel at xray.bmc.uu.se
Wed May 21 08:24:01 CEST 2003
On Wed, 2003-05-21 at 06:26, PeiQuan Chen wrote:
> Dear gmx-users:
> >> CH3
> >> |
> >> Ph-C-OH. (R.S)
> >> |
> >> Dummy atom
> >> I want to know how to use Dummy atom to represent the molecule.
> >> Can anyboby give me some hints to how the creat the latter molecular top files? Because I haven't
> >> any experience on use the dummy atoms, I wish you can give me a example top file for it.
> >I don't see that you need dummy atoms. If you use united atoms, there is no
> >hydrogen atom attached to the central Carbon; it will be a 'CH1' atom type,
> >e.g. a Carbon-Hydrogen united atom. You do noeed to add an improper
> >dihedral to keep the right tetrahedral arrangement of the Ph, CH3 and OH
> >groups around the central C. (You'll probably want 2 topologies, one R and
> >one S).
> Thank you for your help!
> Yes, I can add an improper dihedral to keep the right tetrahedral arrangement of the Ph,CH3 and OH
> groups arounds the cetral C. But when I want to make a mutation of R-->S or S-->R. How can I define
> the topology files? Can you help me and give me the topology files.
> By the way, If I want to add improper diheral to keep, How to define the two different improper dihedral
> in the topology files. Can you give me the topology files?
> I haven't any experiment on make this type improper diheral! Please help me with a example files.
put your molecule (the above drawing) in the prodrg server and check the
topology for one molecule. Then find the improper you need to change.
Going from R->S probably means just modifying the sign of the angle in
the improper, so that would be
A B C D 1 -35 160 35 160
check manual chapter 5 and turn on free energy stuff.
> Thank you in advance.
> Sincerely yours
> PeiQuan Chen
> PeiQuan Chen Department of Chemistry, Nankai University
> WeiJin Road 94, TianJin, 300071, P.R.China
> phone: (86)2223506728 Mobile Phone: (+86)13920675030
> gromacs at 163.com
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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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