[Chimera-users] dock prep multiple models
Elaine Meng
meng at cgl.ucsf.edu
Mon Jun 14 11:00:08 PDT 2010
Hello Francesco,
You do not want them together in one molecule, you want two separate molecules. You could use the combined single PDB input (the corrected version that gives two separate models), but when saving the Mol2 file, choose the option to save multiple models in "a single file [individual @MOLECULE sections]"
Elaine
On Jun 14, 2010, at 10:48 AM, Francesco Pietra wrote:
> Hello Elaine:
> Corrected my mistake, for methane and ethane as a simple example of
> multiple ligands, I run dockprep
>
> (1) for each molecule singularly, then concatenating the two mol2 file
> with "cat". Here the result (between ***)
>
> ***************************
> @<TRIPOS>MOLECULE
> MTH.pdb
> 5 4 1 0 0
> SMALL
> AMBER ff99SB
>
>
> @<TRIPOS>ATOM
> 1 C -0.3700 -0.2620 0.0000 c3 1 MTH -0.1088
> 2 H 0.7430 -0.2620 0.0000 hc 1 MTH 0.0267
> 3 H -0.7410 -0.7870 0.9090 hc 1 MTH 0.0267
> 4 H -0.7410 -0.7870 -0.9090 hc 1 MTH 0.0267
> 5 H -0.7420 0.7870 0.0000 hc 1 MTH 0.0267
> @<TRIPOS>BOND
> 1 1 2 1
> 2 1 3 1
> 3 1 4 1
> 4 1 5 1
> @<TRIPOS>SUBSTRUCTURE
> 1 MTH 1 RESIDUE 4 A MTH 0 ROOT
> @<TRIPOS>MOLECULE
> ETH.pdb
> 8 7 1 0 0
> SMALL
> AMBER ff99SB
>
>
> @<TRIPOS>ATOM
> 1 C -0.7570 -0.1130 -0.0040 c3 1 ETH -0.0941
> 2 C 0.7570 0.1130 0.0040 c3 1 ETH -0.0941
> 3 H -0.9980 -1.2020 -0.0060 hc 1 ETH 0.0317
> 4 H -1.2340 0.3420 0.8950 hc 1 ETH 0.0317
> 5 H -1.2250 0.3430 -0.9070 hc 1 ETH 0.0317
> 6 H 1.2250 -0.3430 0.9070 hc 1 ETH 0.0317
> 7 H 1.2340 -0.3410 -0.8950 hc 1 ETH 0.0317
> 8 H 0.9980 1.2020 0.0060 hc 1 ETH 0.0317
> @<TRIPOS>BOND
> 1 1 2 1
> 2 1 3 1
> 3 1 4 1
> 4 1 5 1
> 5 2 6 1
> 6 2 7 1
> 7 2 8 1
> @<TRIPOS>SUBSTRUCTURE
> 1 ETH 1 RESIDUE 4 A ETH 0 ROOT
> **************************************
>
> (2) on the combined pdb file (result between &&&)
>
> &&&&&&&&&&&&&&&
> @<TRIPOS>MOLECULE
> MTH.ETH.pdb (combined)
> 13 11 2 0 0
> SMALL
> NO_CHARGES
>
>
> @<TRIPOS>ATOM
> 1 C -0.3700 -0.2620 0.0000 c3 1 MTH -0.1088
> 2 H 0.7430 -0.2620 0.0000 hc 1 MTH 0.0267
> 3 H -0.7410 -0.7870 0.9090 hc 1 MTH 0.0267
> 4 H -0.7410 -0.7870 -0.9090 hc 1 MTH 0.0267
> 5 H -0.7420 0.7870 0.0000 hc 1 MTH 0.0267
> 6 C -0.7570 -0.1130 -0.0040 c3 2 ETH -0.0941
> 7 C 0.7570 0.1130 0.0040 c3 2 ETH -0.0941
> 8 H -0.9980 -1.2020 -0.0060 hc 2 ETH 0.0317
> 9 H -1.2340 0.3420 0.8950 hc 2 ETH 0.0317
> 10 H -1.2250 0.3430 -0.9070 hc 2 ETH 0.0317
> 11 H 1.2250 -0.3430 0.9070 hc 2 ETH 0.0317
> 12 H 1.2340 -0.3410 -0.8950 hc 2 ETH 0.0317
> 13 H 0.9980 1.2020 0.0060 hc 2 ETH 0.0317
> @<TRIPOS>BOND
> 1 1 2 1
> 2 1 3 1
> 3 1 4 1
> 4 1 5 1
> 5 6 7 1
> 6 6 8 1
> 7 6 9 1
> 8 6 10 1
> 9 7 11 1
> 10 7 12 1
> 11 7 13 1
> @<TRIPOS>SUBSTRUCTURE
> 1 MTH 1 RESIDUE 4 A MTH 0 ROOT
> 2 ETH 6 RESIDUE 4 A ETH 0 ROOT
> &&&&&&&&&&&&&&&&
>
>
> Could you imagine if providing the resulting mol2 file from method (1)
> or method (2) to DOCK6.4 will be equivalent or should I continue the
> example by actually docking? Unfortunately I have no receptor for my
> (bad) chosen example.
>
> With the combined pdb file, does dockprep operate on single molecules
> one after the other, so that it will not encounter obstacles even for
> many (more complex) ligands?
>
> Thanks
> francesco
>
>
>
>
> On Mon, Jun 14, 2010 at 6:01 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 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
>>
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