Dear Fabrício,
The derivation of RESP or ESP charges and the generation of force
field library(ies) for the different fragments of a modified
amino-acid are now automatically handled by R.E.D. Server. By
providing a single P2N file for the dipeptide (ACE-XXX-NME; XXX =
modified amino-acid) of a modified amino-acid a researcher can use
R.E.D. Server/R.E.D. IV to generate the force field libraries and
charge values for the Central, the N-terminal and C-terminal fragments
as well as for the dipeptide molecule in a single approach/R.E.D. IV
job.
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
versus
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
At the end the user get a set of mol2 files to be loaded in LEaP (a
new force field library file format is going to be proposed soon).
We also have by now the scripts for the direct submission of the data
generated by R.E.D. and/or R.E.D. Server in the reviewing process of
R.E.DD.B.
regards, Francois
PS In these particular case (not true for nucleotide fragments) if the
total charge of each fragment/dipeptide is not an integer value this
likely means the constraints used during the charge fitting step to
define the different molecular fragments are wrong, or are not
correctly set up in the RESP input. Just use this new R.E.D. Server
feature as all is done automatically...
Quoting Fabrício Bracht <bracht.iq.ufrj.br>:
> Hello. I am trying to create new parameters for a new acetylated
> serine (acetylated on the sidechain OH). I've tried to follow some of
> the previous instructions I got here on the mailing list. Here is a
> brief excerpt from a previous answer I got:
>
> I suggest you create a new amino acid: an actylated serine. Give it a
> unique name and change the protein pdb file to reflect this name at the
> appropriate serine (you should delete the hydroxyl hydrogen, also.)
> You may have to remove the water to have room for the acetyl group
> (but even then it may not fit.) You can just leave the atoms of the
> serine (minus hydrogen), and leap will fill in the acetyl group with
> geometry as specified by the new residue descriptor file (which can be
> of various formats: mol2 file, .off library file, or prep file.)
>
> There are two main approaches to new residue generation: antechamber and
> RED. See postings in this mailing list for pointers. Several people
> have posted about generating phosphorylated serine residues, for
> example.
>
> This suggestion helped me in 90% of the way. The problem is that the
> sum of the charges in my new aminoacid is somewhat wrong. Here is what
> I've been trying to do.
> I've created a new residue by the name SAC. This is my serine residue
> which contains my serine frame plus my acetyl group attached to the
> sidechain OH (without the H obviously).
> In order to calculate the partial charges of this residue, I had to
> end-cap it with an NME and a ACE groups. These groups are there to
> substitute the missing bonds I generated when I removed the residue
> from the protein. So, what I actually submit for my RESP calculation
> is a serine residue with an extra methyl group at my N and an extra
> methyl group at my C terminus, plus my C=O(CH3) group attached to the
> O of my former sidechain OH.
> After I examine the resulting partial charges, I see that, once I
> eliminate my endcaps, the total sum is -0.5454. This means that once I
> rejoin my custom aminoacid with my protein, the total sum is -1.5454.
> Something is wrong here and probably is by something I am doing wrong.
> Some help here would really be appreciated.
>
> Fabrício
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Received on Wed Sep 21 2011 - 09:00:02 PDT
