[gmx-users] How to calculate the COM and box vectors in umbrella sampling
Maziya Ibrahim
maziya.ibrahim at gmail.com
Mon Jul 14 11:48:45 CEST 2014
Thank you for the reply and clarifications.
As I mentioned I want to use a protein-ligand complex as starting structure
for the US simulations. My pdb file coordinates after running regular MD is
like so:
TITLE Protein in water
REMARK THIS IS A SIMULATION BOX
CRYST1 121.660 121.660 121.660 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 N MET 1 94.670 85.550 30.870 1.00
0.00
ATOM 2 H1 MET 1 94.420 86.450 30.490 1.00
0.00
ATOM 3 H2 MET 1 95.360 85.740 31.570 1.00
0.00
ATOM 4 H3 MET 1 95.170 85.100 30.130 1.00
0.00
ATOM 5 CA MET 1 93.480 84.830 31.330 1.00
0.00
ATOM 6 CB MET 1 93.780 83.330 31.470 1.00
0.00
ATOM 7 CG MET 1 92.600 82.360 31.420 1.00
0.00
ATOM 8 SD MET 1 91.600 82.470 32.940 1.00
0.00
ATOM 9 CE MET 1 92.600 81.570 34.100 1.00
0.00
ATOM 10 C MET 1 92.900 85.380 32.640 1.00
0.00
ATOM 11 O MET 1 93.370 84.960 33.700 1.00
0.00
............................. (Cont'd)
ATOM 2418 1HD2 ASN 245 84.700 92.730 16.110 1.00
0.00
ATOM 2419 2HD2 ASN 245 83.050 92.490 16.650 1.00
0.00
ATOM 2420 C ASN 245 85.290 91.320 11.590 1.00
0.00
ATOM 2421 O1 ASN 245 85.350 92.260 10.770 1.00
0.00
ATOM 2422 O2 ASN 245 86.340 90.700 11.870 1.00
0.00
ATOM 2423 C1 UNL 246 63.920 76.740 32.640 1.00
0.00
ATOM 2424 C10 UNL 246 62.670 77.230 31.920 1.00
0.00
ATOM 2425 O12 UNL 246 63.010 77.210 30.530 1.00
0.00
ATOM 2426 C13 UNL 246 62.540 76.160 29.810 1.00
0.00
ATOM 2427 O3 UNL 246 61.390 76.200 29.360 1.00
0.00
ATOM 2428 C5 UNL 246 63.570 75.060 29.560 1.00
0.00
ATOM 2429 C6 UNL 246 63.090 73.730 28.980 1.00
0.00
ATOM 2430 C14 UNL 246 64.140 72.840 28.820 1.00
0.00
ATOM 2431 C9 UNL 246 64.070 71.590 29.410 1.00
0.00
ATOM 2432 H9 UNL 246 63.240 71.350 30.080 1.00
0.00
ATOM 2433 C7 UNL 246 65.070 73.160 27.840 1.00
0.00
ATOM 2434 H7 UNL 246 65.080 74.110 27.310 1.00
0.00
ATOM 2435 C8 UNL 246 66.030 72.210 27.500 1.00
0.00
ATOM 2436 H8 UNL 246 66.910 72.480 26.920 1.00
0.00
ATOM 2437 C15 UNL 246 65.960 70.960 28.120 1.00
0.00
ATOM 2438 O4 UNL 246 66.940 70.070 27.810 1.00
0.00
ATOM 2439 H4 UNL 246 66.830 69.200 28.290 1.00
0.00
ATOM 2440 C16 UNL 246 65.040 70.640 29.110 1.00
0.00
ATOM 2441 O11 UNL 246 65.090 69.340 29.480 1.00
0.00
ATOM 2442 C2 UNL 246 64.210 68.750 30.450 1.00
0.00
TER
ENDMDL
When I use the command
pdb2gmx -f input.pdb -ignh -ter -o complex.gro
to build the complex as the tutorial mentions, I get an error as such
" Fatal error: Residue 'UNL' not found in residue topology database"
I realize this is because the ligand itp file is not in the directory
in use. Hence I separated the protein and ligand coordinates and
generated a lig.gro and
& lig.itp file from PRODRG, and then incorporated this itp file
topology into topol.top. Is this correct? I am not sure if only the
protein will be restrained
or both the protein and ligand will be restrained during the pulling
simulations?
On Thu, Jul 10, 2014 at 6:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/10/14, 1:47 AM, Maziya Ibrahim wrote:
>
>> Dear all,
>>
>> I want to carry out umbrella sampling on a protein-ligand complex, that
>> was
>> already subjected to regular MD simulation for a few nanoseconds.
>>
>> How should I calculate the optimum pull distance and box size to be used?
>>
>
> The length of the vector should be sufficient to at least preclude
> short-range nonbonded interactions and any water-mediated effects between
> the protein and ligand. It's not possible to achieve total non-interaction
> in a periodic cell with PME.
>
>
> Is there a default value that can be applied?
>>
>
> No.
>
>
> Also how to calculate the center of mass of the protein and the box
>> vectors?
>>
>>
> g_traj -ox -com with suitable index groups will tell you the COM positions
> of anything, though simply using the protein as the reference group may not
> be appropriate, depending on the geometry of the system. The box vectors
> are in the coordinate file, either the final line of a .gro file or the
> CRYST1 line of a .pdb file.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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