[Chimera-users] dock prep multiple models
Francesco Pietra
chiendarret at gmail.com
Mon Jun 14 10:48:51 PDT 2010
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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