[gmx-users] Structure file for di atmoic molecule

[Juliette N.]

Hi Justin,

I have problem obtaining the structure file for the simple di atomic
molecule ethylene. Below is the details of the the steps. First I used
PRODRG to obtain structure of c=c=c=c as:

HETATM    1  CAA DRG     1      13.520  13.910 -14.390  1.00 20.00
C

HETATM    2  CAB DRG     1      13.860  12.680 -14.670  1.00 20.00
C

HETATM    3  CAC DRG     1      14.170  11.540 -14.940  1.00 20.00
C

HETATM    4  CAD DRG     1      14.500  10.310 -15.220  1.00 20.00
C

then I discarded the first and last lines to obtain the double bonded
carbons in the middle (ethylene):

HETATM    1 C2 Ethyelne     1      13.860  12.680 -14.670  1.00 20.00
C

HETATM    2  C1 Ethylene     1      14.170  11.540 -14.940  1.00 20.00
C

This is my Ethylene.pdb.



Now I need to add the following to the rtp and hdb files.

ffoplsaa.hdb:

 Ethylene 2

2       3       H1      C1      C2      ???

2       3       H2      C2      C1      ???

Q 1 ) I am not sure what to enter for the last column for a di atomic
molecule (C=C).?


ffoplsaa.rtp:

 [ Ethylene ]

 [ atoms ]

   C1    opls_136    -0.120    1

   H11   opls_140     0.060    1

   H12   opls_140     0.060    1

   C2    opls_136    -0.120    2

   H21   opls_140     0.060    2

   H22   opls_140     0.060    2



[ bonds ]

   C1    H11

   C1    H12

   C1    C2

   C2    H21

   C2    H22

   C2    C1



Q 2) Also I am not sure if I need the last line which says C2 is connected
to C1, given that in line 3 I have C1 C2 indicating the same thing!

editconf -f Ethylene.pdb -o Ethylene.gro -bt cubic

pdb2gmx -f Ethylene.gro -o Ethylene-pdb2.gro -p Ethylene-pdb2.top -ff
oplsaa >& output.pdb2gmx


but top file contains no information:

Can you please help me with this? Thanks a lot !


;

;    /////////////////////////////////////

;     At date:

;     This is a standalone topology file

;

;     It was generated using program:

;     pdb2gmx - VERSION 4.5.4

;;     Command line was:

;     pdb2gmx -f Ethylene.gro -o Ethylene-pdb2.gro -p Ethylene-pdb2.top -ff
oplsaa

;;     Force field was read from the standard Gromacs share directory.

;

; Include forcefield parameters

#include "oplsaa.ff/forcefield.itp"

 ---------------------------------------


On 31 March 2013 12:24, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/31/13 12:23 PM, Juliette N. wrote:
>
>> Dear gmx users,
>>
>> Does anyone know how to obtain structure file for the simple ethylene
>> molecule ( C-C) ? I tried PRODRG but it fails to generate structure files
>> for di atomic molecules.
>>
>> Any suggestion is appreciated!
>>
>>
> For something as simple as a diatomic molecule, open up your favorite text
> editor and write it by hand :)
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>



-- 
Thanks,
J. N.