If in vacuum, I would add hydrogens via covalent bonds.
Dr. Vitaly V. Chaban
On Mon, Oct 28, 2013 at 10:29 AM, Richa Singh
wrote:
> Hi all,
>
> I'm trying to run a vacuum simulation of my protein which has a non-zero
> charge.
> How to deal with this charge? Can I add counter ions in to my sys
Hi all,
I'm trying to run a vacuum simulation of my protein which has a non-zero charge.
How to deal with this charge? Can I add counter ions in to my system?
Would it be energetically stable?
How can one bring a protein to its isoelectric point?
--
gmx-users mailing listgmx-users@gromacs.or
On Thu, Apr 11, 2013 at 5:09 AM, fantasticqhl wrote:
> Dear GMX users,
>
> Just a simple question, are the Coulomb interactions calculated using
> charges from ffnonbonded.itp or aminoacid.rtp?
>
> Normally, they are the same. However, if I modify some charges for some
> atoms (for example CB) of
Dear GMX users,
Just a simple question, are the Coulomb interactions calculated using
charges from ffnonbonded.itp or aminoacid.rtp?
Normally, they are the same. However, if I modify some charges for some
atoms (for example CB) of some residues in the aminoacid.rtp,
but do not modify in ffno
Alright, I understand now.
Many thanks for this!
Antoine
Le 29/08/2012 18:57, Mark Abraham a écrit :
On 30/08/2012 3:18 AM, Delmotte, Antoine wrote:
Many thanks for your quick response, Mark.
So epsilon_r is actually different from the actual relative
permittivity (which would be like 80 fo
On 30/08/2012 3:18 AM, Delmotte, Antoine wrote:
Many thanks for your quick response, Mark.
So epsilon_r is actually different from the actual relative
permittivity (which would be like 80 for water), is that right?
You can have an atomistic solvent or a continuum solvent, but not both
at onc
Many thanks for your quick response, Mark.
So epsilon_r is actually different from the actual relative permittivity
(which would be like 80 for water), is that right?
If so, how does one usually chooses this value of epsilon_r? Is the
default value of 1 applicable for most cases (like for sim
On 08/29/2012 11:08 PM, Delmotte, Antoine wrote:
Dear Gromacs users,
I would like to know which charges are used by Gromacs in the
calculation of electrostatic interactions in the standard coulomb
potential:
E_electrostatics = 138.935 * q1 * q2 / (epsilon_r * r_12);
Are q1 and q2 the value
Dear Gromacs users,
I would like to know which charges are used by Gromacs in the
calculation of electrostatic interactions in the standard coulomb potential:
E_electrostatics = 138.935 * q1 * q2 / (epsilon_r * r_12);
Are q1 and q2 the values tabulated in the file "aminoacids.rtp" of the
fo
On 2012-04-02 20:40, R.Perez Garcia wrote:
Dear prof. van der Spoel,
I know.. Dr. Alex de Vries is supervising me for my colloquium.
Unfortunately (for me), they are very busy and (mainly) I am doing four
months stage at Perugia universityv (It) which means I can not
personally ask...so I prefer
Dear prof. van der Spoel,
I know.. Dr. Alex de Vries is supervising me for my colloquium. Unfortunately
(for me), they are very busy and (mainly) I am doing four months stage at
Perugia universityv (It) which means I can not personally ask...so I prefer to
ask the list.
Thank you for your answer
On 2012-04-02 20:29, R.Perez Garcia wrote:
Dear GROMACS users,
I would like to place the charge more localized in the "bonds region"
and not exactly in the atoms.
Please let me know if you know there is a way to do this in GROMACS.
Thank you in advance, R
Yes, using virtual sites.
There's an e
Dear GROMACS users,
I would like to place the charge more localized in the "bonds region" and not
exactly in the atoms.
Please let me know if you know there is a way to do this in GROMACS.
Thank you in advance, R
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman
Tanos Franca wrote:
Dear gmx users,
Does someone know in which file GROMACS store the information on the
protein charge. I've seen that after running pdb2gmx or grompp the
system charge is shown in the screen but we would like to know if this
information is recorded in some file.
I
Dear gmx users,
Does someone know in which file GROMACS store the information on
the protein charge. I've seen that after running pdb2gmx or grompp the
system charge is shown in the screen but we would like to know if this
information is recorded in some file.
With my best regards,
Dear Professor Spoel.
I have a question concerning your article on the SW water model
published in J. Phys. Chem. B, 105, 2618-2626 (2001). I guess the
question is only indirectly related to GROMACS, but I'll post in on the
mailing list since it may be of interest to other GROMACS users as wel
Triguero, Luciano O wrote:
Hi gromacs guru!
Does any know a clever way on how to convert QM charges to group charges as in
shown in the residue topology file?
Nope. You should read the documentation for the force field - probably
the original published manuscript - and see how the others wer
Hi gromacs guru!
Does any know a clever way on how to convert QM charges to group charges as in
shown in the residue topology file?
Ciao,
Luciano
Dr. Luciano Triguero
College of Art and Science
Department of Chemistry
Cox Science Building
1301 Memorial Drive, Room 146
P.O Box 249118
Coral Gabl
Carsten Baldauf wrote:
dear all//
i need to parameterize a non-natural amino acid residue.
i have a problem with assigning the charges, how should i scale them? i
can obtain quantum chemical charges from AM1 to {HF,DFT}/6-31G* and
further, but how to include (scaling, i now where to write them)
the problems gets more difficult to me ... :-(
i want to substitute a single peptide bond in a normal sequence with an
ester bond. i have problems finding the right parameters for an ester
bond, does somebody has done something similar? i would be very happy
about any help.
thanks in advance/
dear all//
i need to parameterize a non-natural amino acid residue.
i have a problem with assigning the charges, how should i scale them? i
can obtain quantum chemical charges from AM1 to {HF,DFT}/6-31G* and
further, but how to include (scaling, i now where to write them) them in
the force fiel
Dmitriy Golubobsky wrote:
Dear Guru,
i need an advice.
i create 3 resudues for my polymer. ( begin-monomer, middle-monomer,
end-monomer)
optimize geometry and charges in gaussin 6-31G.
formalize topology for OPLS force-field.
but, i've got a question
have i to do RESP of the charges of my monom
Dear Guru,
i need an advice.
i create 3 resudues for my polymer. ( begin-monomer, middle-monomer,
end-monomer)
optimize geometry and charges in gaussin 6-31G.
formalize topology for OPLS force-field.
but, i've got a question
have i to do RESP of the charges of my monomers according to ff or not?
i
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