[gmx-users] Polyethylene Surface generation

[Mark Abraham]

----- Original Message -----
From: Yash Gandhi <ydgandhi at gmail.com>
Date: Monday, October 4, 2010 20:32
Subject: [gmx-users] Polyethylene Surface generation
To: gmx-users at gromacs.org

> Hi,
> A few days ago I had posted a request regarding help with Polyethylene surface generation. I had earlier taken help of an older thread to create a gmx file for PE. I also did the modifications in rtp and hdb files as mentioned in the link. After a few thoughts I tried to create a pdb file using some logic. It's as follows:
 > 
> HETATM    1  C1   EtB        1      -4.243   0.027  -1.420 
> HETATM    2  C2   EtB      1      -2.975  -0.719  -0.982 
> HETATM    3  C1   Eth      2      -1.840   0.252  -0.620 
> HETATM    4  C2   Eth      2      -0.566  -0.487  -0.180 
> HETATM    5  C1   Eth      3       0.567   0.487   0.181 
> HETATM    6  C2   Eth      3       1.841  -0.252   0.621 
> HETATM    7  C1   EtE      4       2.976   0.719   0.983 
> HETATM    8  C2   EtE      4       4.244  -0.026   1.420 
> HETATM    9  H11  EtB      1      -5.058  -0.688  -1.680 
> HETATM   10  H12  EtB      1      -4.048   0.659  -2.317 
> HETATM   11  H13  EtB      1      -4.620   0.690  -0.609 
> HETATM   12  H21  EtB      1      -2.642  -1.393  -1.807 
> HETATM   13  H22  EtB      1      -3.213  -1.362  -0.102 
> HETATM   14  H11  Eth      2      -2.179   0.926   0.202 
> HETATM   15  H12  Eth      2      -1.609   0.895  -1.503 
> HETATM   16  H21  Eth      2      -0.227  -1.161  -1.003 
> HETATM   17  H22  Eth      2      -0.797  -1.130   0.702 
> HETATM   18  H11  Eth      3       0.228   1.161   1.003 
> HETATM   19  H12  Eth      3       0.798   1.129  -0.702 
> HETATM   20  H21  Eth      3       2.180  -0.926  -0.202 
> HETATM   21  H22  Eth      3       1.610  -0.895   1.504 
> HETATM   22  H11  EtE      4       2.643   1.393   1.807 
> HETATM   23  H12  EtE      4       3.213   1.362   0.102 
> HETATM   24  H21  EtE      4       5.059   0.688   1.679 
> HETATM   25  H22  EtE      4       4.621  -0.690   0.608 
> HETATM   26  H23  EtE      4       4.050  -0.658   2.317 
> CONECT    1    2 
> CONECT    2    1    3 
> CONECT    3    2    4 
> CONECT    4    3 
> END
> 
> after running pdb2gmx command and taking OPLSAA Force field with the additional residues as mentioned in the link, I am getting the same error always and I am not able to get the reason why
> 
> Fatal error:
>  Atom C1 in residue EtOH 1 not found in rtp entry with 9 atoms
>              while sorting atoms
> 
> Please help me urgently as I am not able to know why is the EtOH residue being used.

EtOH for ethanol is defined in standard OPLS/AA force field files. pdb2gmx is trying to match what you've given it to that, rather than your ethylene .rtp entries. What are your .rtp entries? Have you got your PDB columns correct? Also, perhaps keeping atoms from the same residue adjacent will be a good idea.

Mark

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