On Sep 12, 2011, at 10:16 PM, Bruno Rodrigues wrote:
> Dear Fabrício,
>
> Probably Packmol, from Unicamp is suitable for what you want
> Take a look: http://www.ime.unicamp.br/~martinez/packmol/
>
> I've never used it, but I heard good things about the code, and also the
> developers are very welcome for questions.
>
> Good luck
>
> 2011/9/12 Fabrício Bracht <bracht.iq.ufrj.br>
>
>> I have a protein structure I would like to modify by introducing a ACE
>> group to a serine sidechain. Since this structure comes from a
>> previous simulation, there is a water molecule conveniently placed at
>> that specific position. I guess it would be useful if I could simply
>> substitute this water molecule by the (-(C=O)CH3) fragment. I have
>> read read the tutorial which describes how to create a custom residue,
>> but I would like to know if there is a simpler way of making this type
>> of addition to the structure like a structure editor or even by
>> addition via xleap. The whole "creating a ligand file, approaching
>> manually and bonding via xleap" sounds like too much for something
>> that is not really a ligand. Well, any suggestion is welcome here.
>> Thank you
>> Fabrício
>>
> --
> Bruno Barbosa Rodrigues
> PhD Student - Physics Department
> Universidade Federal de Minas Gerais - UFMG
> Belo Horizonte - Brazil
Whether it is strictly a "ligand" or not is not the issue. There is no
such residue as an actylated serine in any of the AMBER FF data bases
(correct me if I am wrong, folks.) So to have force field parameters,
you will have to follow the prescription for generating a new residue
as outlined by the tutorial or various postings to this mailing list.
Google the list archive for help.
Sorry, but these FF parameters have to come from somewhere. The
parameters are needed to describe the chemistry of the residue. You
can not run classical MD without them.
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.
BTW, using packmol-generated systems for AMBER MD can be problematic.
Google the archives for the caveats involved.
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 Mon Sep 12 2011 - 21:00:02 PDT
