[gmx-users] A topol file of calix[4]pyrrole

[Erik Lindahl]

On Saturday, Mar 1, 2003, at 08:02 US/Pacific, PeiQuan Chen wrote:

> Dear gmx-users(especial Erik,David,Berk)：
>   Recently I want to do some simulation on the molecule 
> meso-octamethyl-calix[4]pyyrole using the oplsaa force field.Becuase 
> the molecule isn't a potein.So I must be write the top file myself.The 
> following is my building to file of the molecule. Becuase I a newer of 
> this program, I can't confirm whether my .top file is write. So I 
> paste the file in here. If it is someting wrong in it, Please correct 
> it.The .pdb file and .mdp file also gived as a attachment! Thank you!
>   Ps:When I use the .top file to do EM.And I got a conformation that 
> is not consistent with the literature. In the literature the molecule 
> 1,3-alternative conformation(just like the calix[4]arene ) is a S4 
> symmetry. But The Gromacs pakages EM result seem the 1,3-alternative 
> distort from the S4 symmetry. Is anything wrong from my .top file!
>

Hi,

Unfortunately I don't have the time to check topologies manually for 
you, but it looks as if you built the topology directly. I would 
definitely recommend creating a building block in the rtp file instead, 
since pdb2gmx can then assign all dihedrals, bonds, angles, etc. 
automatically.

In general, OPLS is rather restrictive with improper dihedrals, but 
check the available OPLS literature to see if they should be use for 
your type of conformations.

Other things to do is to make sure you have the right atom types, check 
the result from the energy minimization (do you get a good energy?), 
and check the energy from a single step to see if you have huge 
energies e.g. in bonds/angles/dihedrals when you start from an 
experimental structure. If you do, locate the faulty interaction by 
testing what happens when you turn the off (basically a binary search).

Cheers,

Erik

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