[gmx-users] polyethelenes

[Zuzana Benkova]

Hello gmx-users,

I have only little experiences with Gromacs and I am trying to run MD
simulations on polyethelenes. I tried to modify the ffoplsaa.rtp and
ffoplsaa.hdb where I have added my own residui. The addition in ffoplsaa.rtp
is as follows

 

; Ethyle - CH3-CH2 the first unit in polyethylenes

[ TTH ]

 [ atoms ]

    C1   opls_135    -0.180    1

   HA1   opls_140     0.060    1

   HA2   opls_140     0.060    1

   HA3   opls_140     0.060    1

    C2   opls_136    -0.120    2

   HB1   opls_140     0.060    2

   HB2   opls_140     0.060    2

 [ bonds ]

   C1    HA1

   C1    HA2

   C1    HA3

   C1    C2

   C2    HB1

   C2    HB2

 

; Ethylene - CH2-CH2 central parts of polyetylens (CnHm)

[ ETH ]

 [ atoms ]

    C1   opls_135    -0.180    1

   HA1   opls_140     0.060    1

   HA2   opls_140     0.060    1

    C2   opls_136    -0.120    2

   HB1   opls_140     0.060    2

   HB2   opls_140     0.060    2

 [ bonds ]

   C1    HA1

   C1    HA2

   C1    C2

   C2    HB1

   C2    HB2

 

; Ethyle - CH2-CH3 the last unit in polyethylenes

[ THT ]

 [ atoms ]

    C1   opls_135    -0.180    1

   HA1   opls_140     0.060    1

   HA2   opls_140     0.060    1

    C2   opls_136    -0.120    2

   HB1   opls_140     0.060    2

   HB2   opls_140     0.060    2

   HB3   opls_140     0.060    2

 [ bonds ]

   C1    HA1

   C1    HA2

   C1    C2

   C2    HB1

   C2    HB2

   C2    HB3

and the addition in ffoplsaa.hdb file is as follows

 

TTH     2

3       4       HA      C1      C2     HB     +C2

2       6       HB      C2      C1     +C1

ETH     2

2       6       HA       C1      -C2    C2

2       6       HB       C2      C1    +C1

THT     2

2       6       HA       C1      -C2    C2

3       4       HB       C2      C1     -C2    HA

 

I have also added these three residui (TTH, ETH, and THT) into
aminoacids.dat file. 

 

 

My attempt to convert the pdb file into the gro and top files using pdb2gmx
I got following error messages 

 

Error in hdb file: nah = 38

line = ''

 

and

 

Fatal error:

Atom HB not found in residue TTH1 while adding hydrogens

The pdb file is attached in this mail. I would be thankful for any help.
Thank you in advance.

Greetings

Zuzana

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