[gmx-users] Re: how to write the correct top file for membrane protein

liang petrucci123 at vip.sina.com
Mon Nov 26 01:54:02 CET 2007

Dear Mark,

Thanks for your advice, but from my understanding, Berger's force field is 
based on OPLS/Amber.
Lipid itp files from Tieleman's website just use the atom type definitions 
from GROMOS87.
And GROMOS87 is out of fashion now.
So thats why i think it would be better to use OPLS for protein and 
"ffgmx.itp" for lipids.
I am not sure whether I misunderstand the usage of Berger's force field, if 
i am wrong,
please give me further instruction.

I hope it would not be bothering you.  Thanks so much!


>> Dear Justin,
>> Thanks for you quickly reply.
>> I have tried before to comment out the section of [ defaults ] in the 
>> next
>> itp file, but still too many warnings and final crashed.
>> And i think it would not be the best method to solve this problem, 
>> because
>> i
>> have to use ffgmx.itp to deal with DPPC.
>> Is there any other method i can try?
> Don't mix forcefields unless you already have hard evidence that this
> combination works - and I'm not aware of any. The link Justin provided
> warns you about that. You need to find a force field that has parameters
> optimized that suit your system. Mixing anything else is about 99% likely
> to make an expensive (and poor) random number generator.
> Mark

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