On Sep 21, 2011, at 12:36 AM, Fabrício Bracht wrote:
> 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
I believe this is mostly automated in the RED approach. Their web site
contains a data base of previous projects, and might even have parameters
for an acetylated serine. I suggest you visit the web site:
http://q4md-forcefieldtools.org/
Look at their data base for acetylated serine parameters. If none are
found, I suggest joining their email list which you should be able to
find somewhere there (I am not a member so do not know for sure.) My
impression is that these people are very helpful and willing to spend
their time to help us succeed in these kinds of projects. In any case,
they have detailed tutorials outlining procedures to do exactly what
you are asking (using their software and tools, of course.) Don't ask
them how to do it with antechamber. They seem to avoid using it. They
invented their own way as a substitute.
They also have a server dedicated to this kind of problem. Using it
will avoid having to acquire/learn an appropriate quantum chemistry
program, and may almost completely automate your project.
Good luck,
Bud Dodson
--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Wed Sep 21 2011 - 06:30:05 PDT
