parameter for phosphonate

Date: Wed Nov 26 2003 - 07:23:45 CST

Dear Jan Saam,
  Thank you for your reply!
  However it is not possible to find any bond P-C because there is only P-O in
Phosphate. Only in Phosponate, there exists bond P-C.

>From: Jan Saam <>
>To: "" <>
>Subject: Re: namd-l: parameter for phosphonate
>First take a look at the parameter file for proteins and lipids, you might
>find parameters for P-C there.
>If it is not there you could take Parameters from a similar configuration i.e.
>P-Carbon from any phosphate (the Carbon just has a different name like CA CB
>C1,...). Copy this entry and change the names accordingly.
>You must decide yourself if the bond you borrow the parameters from is
>chemically equivalent or not.
>Am Mittwoch, 26. November 2003 07:14 schrieben Sie:
>> Dear sir,
>> I want to do MD calculation with NAMD program and CHARMM force field.
>> There is a novel molecule"phosphonate" in my system. I need generate its
>> force field parameter. In CHARMM force field, there are many parameters for
>> nucleic acid. So I can copy many parameters from nucleic acid. However my
>> phosphonate includes bond P-C which nucleic acid have not( it only have
>> bond P-O). Therefore I have to generate the parameters for those including
>> bond P-C such as Kb and b0 in V(bond) = Kb(b - b0)**2, Ktheta and Theta0 in
>> V(angle) = Ktheta(Theta - Theta0)**2 etc. Would you like to give me some
>> advice on these parameter? How should I get these parameters? Or Where can
>> I find these parameter?
>> Thank you very much!

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