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As a new user of NAMD, I am seeking assistance regarding a specific task. I intend to pull a LIGAND from outside to the center of a lipid using NAMD. To achieve this, I have utilized the colvar module with the distance option to measure the separation between two distinct groups: the center of mass of LIGAND and as well the center of mass molecules in the center of the lipid.

In my attempts to exert control over this process, I have employed a harmonic constraint. However, I have encountered an issue where the LIGAND exhibits movement in multiple directions, contrary to my intention of restricting its motion to a single axis, similar to the pull code in GROMACS.

Thus, I am inquiring whether there exists a method within NAMD to confine the axis along which the distance between these two groups decreases.

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1 Answer 1

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You can try steered molecular dynamics (SMD) for this task. Let's say that you have a ligand and an interaction center. You can write out a new PDB file where you set the occupancy of the ligand atoms to a non-zero number. Then you can enable SMD and give this new PDB file as an input, and the pull direction and the pull velocity. For further information please see this link.

Original PDB file

REMARK original generated coordinate pdb file
ATOM      1  N   ARG A   1      -3.903  -0.715  10.177  1.00  0.00      ARG   
ATOM      2  HT1 ARG A   1      -4.767  -0.149  10.323  1.00  0.00      ARG   
ATOM      3  HT2 ARG A   1      -3.899  -0.959   9.163  1.00  0.00      ARG   
ATOM      4  HT3 ARG A   1      -3.865  -1.545  10.788  1.00  0.00      ARG   
ATOM      5  CA  ARG A   1      -2.758   0.230  10.362  1.00  0.00      ARG   
ATOM      6  HA  ARG A   1      -2.778   0.610  11.374  1.00  0.00      ARG   
ATOM      7  CB  ARG A   1      -1.421  -0.522  10.066  1.00  0.00      ARG   
ATOM      8  HB1 ARG A   1      -1.355  -1.413  10.729  1.00  0.00      ARG   
ATOM      9  HB2 ARG A   1      -1.434  -0.874   9.009  1.00  0.00      ARG   
ATOM     10  CG  ARG A   1      -0.139   0.320  10.276  1.00  0.00      ARG   
ATOM     11  HG1 ARG A   1      -0.168   1.193   9.583  1.00  0.00      ARG   
ATOM     12  HG2 ARG A   1      -0.133   0.715  11.316  1.00  0.00      ARG   
ATOM     13  CD  ARG A   1       1.150  -0.455   9.991  1.00  0.00      ARG   
ATOM     14  HD1 ARG A   1       1.243  -1.319  10.687  1.00  0.00      ARG   
ATOM     15  HD2 ARG A   1       1.149  -0.807   8.932  1.00  0.00      ARG   
ATOM     16  NE  ARG A   1       2.293   0.489  10.200  1.00  0.00      ARG   
ATOM     17  CZ  ARG A   1       3.569   0.161  10.024  1.00  0.00      ARG   
ATOM     18  NH1 ARG A   1       3.924  -1.052   9.653  1.00  0.00      ARG   
ATOM     19 HH11 ARG A   1       4.880  -1.272   9.513  1.00  0.00      ARG   
ATOM     20 HH12 ARG A   1       3.208  -1.716   9.484  1.00  0.00      ARG   
ATOM     21  NH2 ARG A   1       4.511   1.061  10.219  1.00  0.00      ARG   
ATOM     22 HH21 ARG A   1       5.463   0.811  10.090  1.00  0.00      ARG   
ATOM     23 HH22 ARG A   1       4.259   1.980  10.500  1.00  0.00      ARG   
ATOM     24  C   ARG A   1      -2.953   1.434   9.416  1.00  0.00      ARG   
ATOM     25  OT1 ARG A   1      -3.891   1.378   8.575  1.00  0.00      ARG   
ATOM     26  OT2 ARG A   1      -2.184   2.415   9.548  1.00  0.00      ARG   
ATOM     27  N   ARG     1      -3.989  -0.713   0.193  1.00  0.00      ARG1  
ATOM     28  HT1 ARG     1      -4.846  -0.133   0.328  1.00  0.00      ARG1  
ATOM     29  HT2 ARG     1      -3.991  -0.983  -0.814  1.00  0.00      ARG1  
ATOM     30  HT3 ARG     1      -3.960  -1.528   0.825  1.00  0.00      ARG1  
ATOM     31  CA  ARG     1      -2.831   0.222   0.350  1.00  0.00      ARG1  
ATOM     32  HA  ARG     1      -2.843   0.628   1.352  1.00  0.00      ARG1  
ATOM     33  CB  ARG     1      -1.506  -0.555   0.070  1.00  0.00      ARG1  
ATOM     34  HB1 ARG     1      -1.449  -1.429   0.755  1.00  0.00      ARG1  
ATOM     35  HB2 ARG     1      -1.526  -0.932  -0.978  1.00  0.00      ARG1  
ATOM     36  CG  ARG     1      -0.212   0.276   0.254  1.00  0.00      ARG1  
ATOM     37  HG1 ARG     1      -0.232   1.132  -0.461  1.00  0.00      ARG1  
ATOM     38  HG2 ARG     1      -0.197   0.697   1.284  1.00  0.00      ARG1  
ATOM     39  CD  ARG     1       1.066  -0.522  -0.016  1.00  0.00      ARG1  
ATOM     40  HD1 ARG     1       1.151  -1.370   0.702  1.00  0.00      ARG1  
ATOM     41  HD2 ARG     1       1.057  -0.901  -1.065  1.00  0.00      ARG1  
ATOM     42  NE  ARG     1       2.222   0.412   0.167  1.00  0.00      ARG1  
ATOM     43  HE  ARG     1       2.026   1.368   0.370  1.00  0.00      ARG1  
ATOM     44  CZ  ARG     1       3.493   0.063  -0.005  1.00  0.00      ARG1  
ATOM     45  NH1 ARG     1       3.831  -1.163  -0.346  1.00  0.00      ARG1  
ATOM     46 HH11 ARG     1       4.784  -1.398  -0.485  1.00  0.00      ARG1  
ATOM     47 HH12 ARG     1       3.106  -1.822  -0.497  1.00  0.00      ARG1  
ATOM     48  NH2 ARG     1       4.447   0.956   0.164  1.00  0.00      ARG1  
ATOM     49 HH21 ARG     1       5.395   0.690   0.038  1.00  0.00      ARG1  
ATOM     50 HH22 ARG     1       4.208   1.884   0.422  1.00  0.00      ARG1  
ATOM     51  C   ARG     1      -3.015   1.404  -0.625  1.00  0.00      ARG1  
ATOM     52  OT1 ARG     1      -3.956   1.338  -1.461  1.00  0.00      ARG1  
ATOM     53  OT2 ARG     1      -2.233   2.378  -0.520  1.00  0.00      ARG1  
END

SMDFile

CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1           1
ATOM      1  N   ARG A   1      -3.903  -0.715  10.177  0.00  0.00      ARG   
ATOM      2  HT1 ARG A   1      -4.767  -0.149  10.323  0.00  0.00      ARG   
ATOM      3  HT2 ARG A   1      -3.899  -0.959   9.163  0.00  0.00      ARG   
ATOM      4  HT3 ARG A   1      -3.865  -1.545  10.788  0.00  0.00      ARG   
ATOM      5  CA  ARG A   1      -2.758   0.230  10.362  0.00  0.00      ARG   
ATOM      6  HA  ARG A   1      -2.778   0.610  11.374  0.00  0.00      ARG   
ATOM      7  CB  ARG A   1      -1.421  -0.522  10.066  0.00  0.00      ARG   
ATOM      8  HB1 ARG A   1      -1.355  -1.413  10.729  0.00  0.00      ARG   
ATOM      9  HB2 ARG A   1      -1.434  -0.874   9.009  0.00  0.00      ARG   
ATOM     10  CG  ARG A   1      -0.139   0.320  10.276  0.00  0.00      ARG   
ATOM     11  HG1 ARG A   1      -0.168   1.193   9.583  0.00  0.00      ARG   
ATOM     12  HG2 ARG A   1      -0.133   0.715  11.316  0.00  0.00      ARG   
ATOM     13  CD  ARG A   1       1.150  -0.455   9.991  0.00  0.00      ARG   
ATOM     14  HD1 ARG A   1       1.243  -1.319  10.687  0.00  0.00      ARG   
ATOM     15  HD2 ARG A   1       1.149  -0.807   8.932  0.00  0.00      ARG   
ATOM     16  NE  ARG A   1       2.293   0.489  10.200  0.00  0.00      ARG   
ATOM     17  CZ  ARG A   1       3.569   0.161  10.024  0.00  0.00      ARG   
ATOM     18  NH1 ARG A   1       3.924  -1.052   9.653  0.00  0.00      ARG   
ATOM     19 HH11 ARG A   1       4.880  -1.272   9.513  0.00  0.00      ARG   
ATOM     20 HH12 ARG A   1       3.208  -1.716   9.484  0.00  0.00      ARG   
ATOM     21  NH2 ARG A   1       4.511   1.061  10.219  0.00  0.00      ARG   
ATOM     22 HH21 ARG A   1       5.463   0.811  10.090  0.00  0.00      ARG   
ATOM     23 HH22 ARG A   1       4.259   1.980  10.500  0.00  0.00      ARG   
ATOM     24  C   ARG A   1      -2.953   1.434   9.416  0.00  0.00      ARG   
ATOM     25  OT1 ARG A   1      -3.891   1.378   8.575  0.00  0.00      ARG   
ATOM     26  OT2 ARG A   1      -2.184   2.415   9.548  0.00  0.00      ARG   
ATOM     27  N   ARG A   1      -3.989  -0.713   0.193  1.00  0.00      ARG1  
ATOM     28  HT1 ARG A   1      -4.846  -0.133   0.328  1.00  0.00      ARG1  
ATOM     29  HT2 ARG A   1      -3.991  -0.983  -0.814  1.00  0.00      ARG1  
ATOM     30  HT3 ARG A   1      -3.960  -1.528   0.825  1.00  0.00      ARG1  
ATOM     31  CA  ARG A   1      -2.831   0.222   0.350  1.00  0.00      ARG1  
ATOM     32  HA  ARG A   1      -2.843   0.628   1.352  1.00  0.00      ARG1  
ATOM     33  CB  ARG A   1      -1.506  -0.555   0.070  1.00  0.00      ARG1  
ATOM     34  HB1 ARG A   1      -1.449  -1.429   0.755  1.00  0.00      ARG1  
ATOM     35  HB2 ARG A   1      -1.526  -0.932  -0.978  1.00  0.00      ARG1  
ATOM     36  CG  ARG A   1      -0.212   0.276   0.254  1.00  0.00      ARG1  
ATOM     37  HG1 ARG A   1      -0.232   1.132  -0.461  1.00  0.00      ARG1  
ATOM     38  HG2 ARG A   1      -0.197   0.697   1.284  1.00  0.00      ARG1  
ATOM     39  CD  ARG A   1       1.066  -0.522  -0.016  1.00  0.00      ARG1  
ATOM     40  HD1 ARG A   1       1.151  -1.370   0.702  1.00  0.00      ARG1  
ATOM     41  HD2 ARG A   1       1.057  -0.901  -1.065  1.00  0.00      ARG1  
ATOM     42  NE  ARG A   1       2.222   0.412   0.167  1.00  0.00      ARG1  
ATOM     43  HE  ARG A   1       2.026   1.368   0.370  1.00  0.00      ARG1  
ATOM     44  CZ  ARG A   1       3.493   0.063  -0.005  1.00  0.00      ARG1  
ATOM     45  NH1 ARG A   1       3.831  -1.163  -0.346  1.00  0.00      ARG1  
ATOM     46 HH11 ARG A   1       4.784  -1.398  -0.485  1.00  0.00      ARG1  
ATOM     47 HH12 ARG A   1       3.106  -1.822  -0.497  1.00  0.00      ARG1  
ATOM     48  NH2 ARG A   1       4.447   0.956   0.164  1.00  0.00      ARG1  
ATOM     49 HH21 ARG A   1       5.395   0.690   0.038  1.00  0.00      ARG1  
ATOM     50 HH22 ARG A   1       4.208   1.884   0.422  1.00  0.00      ARG1  
ATOM     51  C   ARG A   1      -3.015   1.404  -0.625  1.00  0.00      ARG1  
ATOM     52  OT1 ARG A   1      -3.956   1.338  -1.461  1.00  0.00      ARG1  
ATOM     53  OT2 ARG A   1      -2.233   2.378  -0.520  1.00  0.00      ARG1  
END

NAMD Input Section

SMD           on
SMDFile       merged_smd.pdb
SMDk          1.0
SMDVel        0.005
SMDDir        {0 0 1}
SMDOutputFreq $restartFreq

I am not sure about the format for SMDDir, but you should be able to figure it out.

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  • $\begingroup$ First of all, Thanks for your comment. Can you provide the template input with any pdb and I will adapt the input to my system. In SMD, Do I need to define the center of the lipid? How can I control the move of the LIG to the center of lipid $\endgroup$ Commented Mar 5 at 18:11
  • $\begingroup$ @Abd-ElazeemMohamed I have added a file. $\endgroup$ Commented Mar 5 at 19:04
  • $\begingroup$ Ok. I understand you. One question, now if the distance between my ligand and the center of the lipid is 75 A so how can I confirm that there ligand will move this distance to the center of the lipid because I was doing umbrella sampling. $\endgroup$ Commented Mar 5 at 19:12
  • $\begingroup$ SMDDir {0 0 1} means that the ligand will move away form the site in the +z direction, and if you use SMDDir {0 0 -1} it will move towards the site in the -z direction. $\endgroup$ Commented Mar 5 at 19:16
  • $\begingroup$ If you are doing umbrella sampling, you can specify the direction of motion in the control section of the collars file. if you are doing umbrella sampling, do not do SMD along with that. $\endgroup$ Commented Mar 5 at 19:18

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