[gmx-users] How to calculate the COM and box vectors in umbrella sampling

[Justin Lemkul]

On 7/14/14, 5:48 AM, Maziya Ibrahim wrote:
> 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

Make sure you correct the PRODRG topology; its charges and charge groups are 
going to be unreliable.

> protein will be restrained
> or both the protein and ligand will be restrained during the pulling
> simulations?
>

The restraint potential is applied to whatever groups you assign.  Without 
seeing exactly what you're doing (i.e. post an .mdp file for us), there's no way 
to answer this.

-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

==================================================