[Chimera-users] dock prep multiple models

[Elaine Meng]

Hi Francesco,
Yes, Dock Prep is often used to make a multi-model mol2 file with charges.

Your input PDB file is wrong. You need to put MODEL & ENDMDL around each model.  In your example, you only have one ENDMDL, and the whole thing will be treated as one (strange) model, which is why you get strange charges.  

It will work if your input file is like this:

MODEL
ATOM      1  C   MTH   1        -0.370  -0.262   0.000  1.00  0.00
ATOM      2  H   MTH   1         0.743  -0.262   0.000  1.00  0.00
ATOM      3  H   MTH   1        -0.741  -0.787   0.909  1.00  0.00
ATOM      4  H   MTH   1        -0.741  -0.787  -0.909  1.00  0.00
ATOM      5  H   MTH   1        -0.742   0.787   0.000  1.00  0.00
ENDMDL
MODEL
ATOM      1  C   ETH   1        -0.757  -0.113  -0.004  1.00  0.00
ATOM      2  C   ETH   1         0.757   0.113   0.004  1.00  0.00
ATOM      3  H   ETH   1        -0.998  -1.202  -0.006  1.00  0.00
ATOM      4  H   ETH   1        -1.234   0.342   0.895  1.00  0.00
ATOM      5  H   ETH   1        -1.225   0.343  -0.907  1.00  0.00
ATOM      6  H   ETH   1         1.225  -0.343   0.907  1.00  0.00
ATOM      7  H   ETH   1         1.234  -0.341  -0.895  1.00  0.00
ATOM      8  H   ETH   1         0.998   1.202   0.006  1.00  0.00
ENDMDL

Best,
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 13, 2010, at 7:30 AM, Francesco Pietra wrote:

> Hi:
> I always docked different molecules to the same receptor molecule per
> molecule, by using dockprep in chimera.  Is it possible with dockprep
> to provide DOCK6.4 a single file containing mol2-type data for a
> number of different molecules to dock to the same receptor? That is,
> circumventing submission to the ZINC database server.
> 
> I tried to get mol2 from a small list of molecules, methane and
> ethane, getting wrong charge (-1) for methane. If adjusted to zero,
> antechamber fails.
> 
> The file was
> 
> ATOM      1  C   MTH   1        -0.370  -0.262   0.000  1.00  0.00
> ATOM      2  H   MTH   1         0.743  -0.262   0.000  1.00  0.00
> ATOM      3  H   MTH   1        -0.741  -0.787   0.909  1.00  0.00
> ATOM      4  H   MTH   1        -0.741  -0.787  -0.909  1.00  0.00
> ATOM      5  H   MTH   1        -0.742   0.787   0.000  1.00  0.00
> MODEL
> ATOM      1  C   ETH   1        -0.757  -0.113  -0.004  1.00  0.00
> ATOM      2  C   ETH   1         0.757   0.113   0.004  1.00  0.00
> ATOM      3  H   ETH   1        -0.998  -1.202  -0.006  1.00  0.00
> ATOM      4  H   ETH   1        -1.234   0.342   0.895  1.00  0.00
> ATOM      5  H   ETH   1        -1.225   0.343  -0.907  1.00  0.00
> ATOM      6  H   ETH   1         1.225  -0.343   0.907  1.00  0.00
> ATOM      7  H   ETH   1         1.234  -0.341  -0.895  1.00  0.00
> ATOM      8  H   ETH   1         0.998   1.202   0.006  1.00  0.00
> ENDMDL
> 
> Thanks
> francesco pietra