Re: [gmx-users] topology transformation

[Christian Burisch]

Anthony Cruz wrote:

Hi users:


Hi Anthony,

How I can convert a topology generated by PRODRG topology generation server to 
a gromos topology??? or I cant use it with the G43a1 GROMOS96 43a1 
Forcefield


did you try the beta version? It generates 43A1 topologies. There are 
some issues with impropers and atom types in phosphate groups (see my 
comment on this list a few months ago), but everything else IMHO is 
parameterized very well. The charges sometimes aren't polar enough 
(e.g. in hydroxyl groups), thus you should use standard 43A1 charge 
group charges as far as possible. For unknown moieties you may need to 
do some QM calculations (e.g. DFT/ESP).


Regards

Christian
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Re: [gmx-users] topology transformation

[Anton Feenstra]

Anthony Cruz wrote:


Hi users:
How I can convert a topology generated by PRODRG topology generation server to 
a gromos topology??? or I cant use it with the G43a1 GROMOS96 43a1 
Forcefield


There is no automatic way to do that. You'll have to assign Gromos atom 
types (which are similar to those from ProDrg, but *not* identical!) and 
bonded types (for bonds, angles, dihdedrals and impropers). You may have 
to check (or add) the exclusions also.


You could use my 'Topology Tools' (see contributions section) to make 
life easier. After you assign atom types, you use nr2nametop to change 
all atom numbers into labels that include the atom names and types. 
Then, e.g., bonds in your itp file will look like:


[bonds]
  CA(CH3) C(C)  
  C(C) O(O) 

Then, using the comments in the ffG43a1bon.itp file, like:
#define gb_40.1230  1.6600e+07
; C  - O1200

you can easily guess to assign gb_4 to the second bond. And, yes, it 
would be possible to automate this to some extent, but it woulc be 
dangerous, too. Assigning bonded interactions like this is really 
guesswork, you will have a good starting point for a molecular topology, 
but (important and/or crucial) details may be horribly wrong.

In practice, it usually works very well, though...

--
Groetjes,

Anton

* NOTE: New Affiliation, Phone & Fax numbers (below) *
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[gmx-users] topology transformation

[Anthony Cruz]

Hi users:
How I can convert a topology generated by PRODRG topology generation server to 
a gromos topology??? or I cant use it with the G43a1 GROMOS96 43a1 
Forcefield

thanks
Anthony
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