[gmx-users] Re: Re: help with chromophore of a GFP

[Anna MARABOTTI]

Dear Mark, Justin and other gmx-users,
 thank you very much for your
help. Thanks to your suggestions, I made some steps forward, but still I
don't see the end of my travel...

 First of all, I would like to say
that my previous problem was solved when I renamed O1 to OA. Justin was
right. When I did it, no other error messages came from pdb2gmx
(including the "long bond" warning). 

Now...let's go to the following
problem... :'( After pdb2gmx, editconf, genbox, here I am with grompp...
When I made it, the fatal error was a list of No default Bond types No
default angle types No default Proper Dih. types No default Improper
Dih. types all referred to CFY, obviously. I know what the problem is, I
don't know how to solve it. I did not add bonded types to ffbonded.itp
because I was sure they all were present. Instead, there are some bonds
that are not present. I have the parameters calculated for these bonds
by Antechamber suite, but I don't know how to convert their format to
the format required by ffbonded.itp. For example, this is the entry I
have for a CT-CT bond in the output coming from Antechamber: 

CT-CT
303.10 1.535 same as c3-c3 

and this is the entry for a CT-CT bond in
ffbonded.itp: 

CT CT 1 0.15260 259408.0 ; 7,(1986),230; AA, SUGARS 

I
can imagine that 1.535 and 0.15260 is the bond length (in A in the first
case, in nm in the second case) and they are more or less identical. But
how can I obtain the second value in ffbond.itp (the kb in kJ mol-1
nm-2) from the data I have? I don't recognize at all the value...

I
know that this is not strictly referred to Gromacs, anyway could you
please tell me at least how can I find information on how to add these
parameters properly? 

Anna


______________________________________________
Anna Marabotti,
Ph.D.
Assistant Professor
Department of Chemistry and Biology
University
of Salerno
Via Ponte don Melillo
84084 Fisciano (SA)
Italy
Phone: +39
089 969583
Fax: +39 089 969603
E-mail: amarabotti at unisa.it
Skype:
annam1972

"When a man with a gun meets a man with a pen, the man with
the gun is a dead man"
(Roberto Benigni, about Roberto Saviano)
 Il
21/03/2013 21:53, gmx-users-request at gromacs.org [1] ha scritto: 




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