[gmx-users] compound-I/II topology, i.e. porphyrin(Fe=O)

Arturas a3arzi at vaidila.vdu.lt
Fri Apr 9 13:10:01 CEST 2004

I see no huge difficulties with charges as they, as you mentioned,
can be calculated with ab initio or semiempyrical methods. 

However, there is b0 and kb konstants in *.rtp file concerning bond
description. How are they optional ?

In general talking abaout topology writing (*.rtp), there is some
missunderstanding. There are fields [bond], [exclusions], [angles],
[dihedrals], [impropers]. Are they all necceassary ?

What are [impropers] needed for ?
[angles] and [dihedrals] have parameters like: th0, cth and phi0, cp,
mult. What are these ? Should I define them too ?


DvdS> On Fri, 2004-04-09 at 10:35, Arturas wrote:
>> Hi,
>> I want to make a topology file for heme with oxygen atom bound to Fe,
>> i.e. compound-I/II model of oxireductases. PRODRG server supports N,
>> C, O, S, P, Cl, I, Br, F atoms only. So PROFRG can not help me. How to
>> solve that problem.
>> Should it be done by hand modifying standart heme tolopogy ? What are
>> parameteres for >Fe=O fragment ?

DvdS> Yes, you can do it in the rtp file. Parameters are the problem, although
DvdS> there must be some quantum calculations done on similar systems, from
DvdS> which you should be able to deduce charges.
>> Any tricks and advises.
>> Arturas

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