[Chimera-users] << creating MOL2 files with different SET records >>

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 3 11:37:24 PDT 2014


Hello Hatuey,
Mostly not…. the only similar option in the Save Mol2 dialog (File… Save Mol2) is

"Write current selection to @SETS section of file"

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#mol2>

This option is mainly for use with DOCK, to specify the rigid part of a small molecule that will be used as a docking ligand.  Example:

@<TRIPOS>SET
ANCHOR          STATIC     ATOMS    <user>   **** Anchor Atom Set
13 53 25 24 23 22 21 20 19 18 17 16 55 54
RIGID           STATIC     BONDS    <user>   **** Rigid Bond Set
12 54 53 52 51 50 49 48 47 46 45 44 43

Best regards,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 2, 2014, at 2:37 PM, Hatuey Hack <hatuey_hack at yahoo.com.br> wrote:

> Hello,
> I will like to know if it is possible with Chimera to create MOL2 files that include other MOL2 records like these:
> 
> @<TRIPOS>SET
> ATOM$BY_TYPE    STATIC     ATOMS    COLORGROUP SYSTEM 
> 5 1 2 3 4 5
> LINK_HS         STATIC     ATOMS    <user>   **** 
> 4 2 3 4 5
> @<TRIPOS>NORMAL
> @<TRIPOS>FF_PBC
> FORCE_FIELD_SETUP_FEATURE Force Field Setup information
> v1.0  0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 NONE 2 0 0 0 0 0 0 0 0 0 0 0 0
> 
> Best regards,
> Hatuey




More information about the Chimera-users mailing list