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