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

[Mark Abraham]

On Fri, Mar 22, 2013 at 2:36 PM, Anna MARABOTTI <amarabotti at unisa.it> wrote:

>
> 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).
>

OK, that's doubly good news.

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...
>

You'll have to start with the Antechamber documentation to find out the use
of and dimensions for those numbers. I have no idea at all, but I'd not be
surprised to hear that it was kcal mol-1 A-2 and perhaps a stray factor of
2 missing from the equation in which it works. That would account for the
factor of ~800 you see here.

You have the option of editing ffbonded.itp (so the lookup from [bonds] is
done via the two atom numbers, which index into [atoms] to get the two atom
names, which index into [bondedtypes]) or on the relevant line of [bonds]
(just dumping the same function type and parameters you'd use in
ffbonded.itp). What to do depends how much you plan to re-use the output of
Antechamber.

Mark


> 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:
>
>
>
>
> Links:
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