On 7/8/12 7:10 AM, Shima Arasteh wrote:
Because I saw that residues defined in aminoacids.rtp file don't have H in
their carboxyl and atom N. So I decided to remove H !
Chemically, there is never an H atom on the C-terminal carbonyl of a group
involved in a peptide bond. If you parameterized a molecule that was protonated
in such a way, it will give an erroneous output. You can't just delete atoms,
and shifting the charge by adding it back somewhere else is also very suspect,
because you're changing the electronic nature of the compound.
I would say you need a better parameterization protocol using a more suitable
model compound.
-Justin
Sincerely,
Shima
________________________________
From: francesco oteri <francesco.ot...@gmail.com>
To: Shima Arasteh <shima_arasteh2...@yahoo.com>
Cc: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Sunday, July 8, 2012 3:28 PM
Subject: Re: [gmx-users] define a new residue
Why have you removed the hydrogen?
2012/7/8 Shima Arasteh <shima_arasteh2...@yahoo.com>
Dear Francesco,
Thanks. Honestly I thought about this, but I don't know how much charges I need
to increase or decrease of other atoms?
Is it possible to add the FVAL with the H atom( which I removed before)? I mean
that I apply the complete formyl-valine and don't remove the H atom.
Thanks for your suggestions.
Cheers,
Shima
________________________________
From: francesco oteri <francesco.ot...@gmail.com>
To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
Sent: Sunday, July 8, 2012 3:04 PM
Subject: Re: [gmx-users] define a new residue
Hi Shima,
usually charge calculation are carried out on the system that is supposed to be
used in the MD.
So in my opinion you shouldn't remove the hydrogen.
Anyway, if you wanna remove the hydrogen, either you increase the charge of
some other atom or
calculate the charges on the new residue without hydrogen.
Francesco
2012/7/8 Shima Arasteh <shima_arasteh2...@yahoo.com>
Hi dear gmx friends,
I got the parameters of formyl-valine through the CHARMM website. Now I need to
define it as a new residue FVAL( as Justin suggested me earlier) in .rtp file.
To set the correct charges for atoms, I used the CHARMM output. In order to
define FVAL to rtp file, I added these lines as below:
CN C 0.349 0
ON O -0.494 1
H1 HC 0.100 2
N NH1 -0.423 3
HN H 0.09 4
CA CT1 0.144 5
HA HB 0.09 6
CB CT1 -0.097 7
HB HA 0.09 8
CG1 CT3 -0.268 9
HG11 HA 0.09 10
HG12 HA 0.09 11
HG13 HA 0.09 12
CG2 CT3 -0.268 13
HG21 HA 0.09 14
HG22 HA 0.09 15
HG23 HA 0.09 16
C C 0.209 17
O O -0.395 18
As you see I omitted the H connected to Carboxyl. Now the total charge of the
new-defined residue is not zero (-0.333) . How can I correct it?
I would appreciate you for your suggestions.
Thanks in advance.
Sincerely,
Shima
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Cordiali saluti, Dr.Oteri Francesco
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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