You don't. CGenFF is a forcefield, like CHARMM36. You install it, add rtp
entries then use pdb2gmx to generate a ligand's topology .itp file
On 2012-12-26 11:35:46AM +0100, Albert wrote:
hello:
I found the script charmm2gromacs-pvm.py
I don't know.
Parachem outputs stuff like this (CHARMM toppar format):
(propionic acid, C3H2O5)
RESI PROA -1.00
GROUP
ATOM C2 CG321 -0.28
ATOM C1 CG2O30.62
ATOM H21 HGA2 0.09
ATOM H22 HGA2 0.09
ATOM O1 OG2D2 -0.76
ATOM O2 OG2D2
of pdb2gmx?
James
2012/12/20 Peter C. Lai p...@uab.edu:
(As a side note, Gromacs shouldn't use charge groups when using
all-atom charmm forcefields.)
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topology for the ligands in charmm27 ff). So
because receptor and bilayer will be parametrized in charmm36 I'm not
sure about proper working of Swiss's topology with that complex.
James
2012/12/19 Peter C. Lai p...@uab.edu:
http://cesium.hyperfine.info/~peter/gromacs/popc36/
has a fully
On 2012-12-19 10:16:09AM +0530, Archana Sonawani wrote:
Hi,
I want to simulate a peptide using SDS micelle. The peptide is random
coil,
but I want it to be helical; therefore, I will use TFE for inducing
helix.
You use TFE in a wet lab to physically induce helicity in real life. For
http://cesium.hyperfine.info/~peter/gromacs/popc36/
has a fully gromacs compatible charmm36 238 POPC bilayer with 21524 waters
On 2012-12-18 09:07:22PM -0800, James Starlight wrote:
Justin, thanks again.
As I understood gromacs already had had parameters for charmm lipid so
the main approach
in the system but How can I find the overlapping atoms
and the reason of clashe among a vast number of atoms?
Sincerely,
Shima
- Original Message -
From: Peter C. Lai p...@uab.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com
Cc: Discussion list for GROMACS users gmx-users
Where is the .itp file for the system?
On 2012-12-15 01:40:27PM -0800, fatemeh ramezani wrote:
hi
I'm simulating gold atom interaction with aminoacidcys. I have made
gold-cys.pdb by hyperchem software:
HETATM 1 N CYS 1 0.000 1.335 0.000
HETATM 2 CA CYS 1
It depends on what the atom is overlapping with and some conjecture as to
what might be causing the overlap:
You can always manually move it, either by editing the .gro file directly
or using a tool like VMD to move it or the molecule/fragment it's attached to
with the mouse and then display the
them, I may get some
other clashes, may I not?
Any other suggestion?
Thanks.
Sincerely,
Shima
- Original Message -
From: Peter C. Lai p...@uab.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Sunday
Not if you aren't going to run those. I assume nvt.mdp and npt.mdp are
restrained runs to remove/dampen clashes and prevent crashes but if you are
already running a full md simulation then you don't need to redo those steps.
Also, I don't use DispCorr for C36 lipids (some debates about that can
On 2012-12-08 03:20:54AM -0800, James Starlight wrote:
1- on what assumptions that blocks were generated ?
This appears to be a swissparm-specific question. I don't know what
algorithms it uses to match what are essentially pharmacophores in the new
molecule with the common individual blocks it
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There is nothing stopping you from replacing the ion in your binding
pocket with the original water and then replacing another water elsewhere
with the ion at the oxygen's coordintes, then running genconf to renumber
the gro file.
On 2012-11-26 06:25:47PM -0800, Yun Shi wrote:
I did hope the
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the trajectory on an atom near the starting COM would minimize
distances traveled due to COM diffusion through the solvent.
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of the manual seems to say
that in type 9, phi_s, k_phi, and the multiplicity are specified. Does this
mean that cp corresponds to the force constant k_phi?
Yes, although the CHARMM people call it KChi.
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On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote:
On 10/18/12 2:43 PM, klexa wrote:
Hi Gromacs users,
I think I am a bit confused about the proper way to handle boxes that are
not
standard cubes. I'm trying to run a membrane simulation where a cyclic
undecapeptide is inserted
On 2012-10-18 03:58:22PM -0400, Justin Lemkul wrote:
On 10/18/12 3:55 PM, Peter C. Lai wrote:
On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote:
On 10/18/12 2:43 PM, klexa wrote:
Hi Gromacs users,
I think I am a bit confused about the proper way to handle boxes
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(205
). I can change the charge in the top file, yet I do not
know how to change sigma and epsilon values.
Best regards,
Cuong
On 15 October 2012 13:57, Peter C. Lai p...@uab.edu wrote:
It's hard to understand your question. What do you mean by reference
parameters? You said you already
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If you have significant temperature fluctuations they will, by definition...
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,
is reporting the results in a paper. How would it be?
Thanks for your suggestion Peter.
Sincerely,
Shima
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To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Wednesday, October 3, 2012 5:16 PM
Subject: Re: [gmx
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to some extent.
You'll probably want to look for yourself to see if your use-case is supported.
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a problem?
I am really thankful for the big amount of help. Thank you.
Lara
- Ursprüngliche Message -
Von: Peter C. Lai p...@uab.edu
An: Discussion list for GROMACS users gmx-users@gromacs.org
CC: Lara Bunte lara.bu...@yahoo.de
Gesendet: 22:13 Freitag, 21.September 2012
-rescale
tc-grps = ISO SOL
tau_t = 0.1 0.1
ref_t = 300 300
pcoupl = no
Greetings
Lara
- Ursprüngliche Message -
Von: Peter C. Lai p...@uab.edu
An: Lara Bunte lara.bu...@yahoo.de
CC: gmx-users@gromacs.org gmx
: Peter C. Lai p...@uab.edu
An: Discussion list for GROMACS users gmx-users@gromacs.org
CC:
Gesendet: 17:43 Montag, 24.September 2012
Betreff: Re: [gmx-users] About mdrun -nt number
# of mdrun threads
-nt N is used to basically tell mdrun how many threads to spawn on the
local host. We
-
Von: Peter C. Lai p...@uab.edu
An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users
gmx-users@gromacs.org
CC:
Gesendet: 17:58 Montag, 24.September 2012
Betreff: Re: [gmx-users] About mdrun -nt number
A thread is like a process. (Except not all threads have
= no
I am totaly frustrated and shortly for giving it up :-(:-( :-(
Best greetings
Lara
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Von: Peter C. Lai p...@uab.edu
An: Lara Bunte lara.bu...@yahoo.de
CC: gmx-users@gromacs.org gmx-users@gromacs.org
Gesendet: 17:57 Montag, 24
On 2012-09-24 12:34:53PM -0400, Justin Lemkul wrote:
On 9/24/12 12:31 PM, Peter C. Lai wrote:
As I noted before, you can safely ignore the gromacs notices when setting
them to the correct cutoffs I listed.
Agreed. Please use the cutoffs that have been posted explicitly 3-4 times
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(205
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was...
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steps
are conducted. (also when certain features may be implemented differently,
such as the introduction of the v-rescale thermostat).
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On 2012-09-06 02:46:21PM +0200, Bogdan Costescu wrote:
On Wed, Sep 5, 2012 at 8:37 PM, Peter C. Lai p...@uab.edu wrote:
Could be a result of not setting x/y compressibility = 0 as the manual
suggests you should do...
As one who has also tried to use walls recently, I've also found
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or sd integrators.
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-POPC system:
To insert a protein in lipid bilayer, I am suggested to simulate POPC in
water separately before insertion, it might decrease the time of final
simulation. It's OK!
In the article suggested me by dear Peter C. Lai, I read that POPC was
simulated in anisotropic pressure
;gen_temp= 300 ; temperature for Maxwell distribution
;gen_seed= -1; generate a random seed
nstcomm = 1
comm_mode = Linear
comm_grps = POPC SOL
On 2012-08-16 09:32:17PM -0500, Peter C. Lai wrote:
You always use semi-isotropic for bilayer work
.
This is where I asked the question about.
Thanks.
Sincerely,
Shima
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From: Peter C. Lai p...@uab.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Friday, August 17, 2012 7:17 AM
, you should be fine.
Sincerely,
Shima
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To: Shima Arasteh shima_arasteh2...@yahoo.com
Cc: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Friday, August 17, 2012 8:19 AM
Subject: Re: [gmx-users] Protein-POPC
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2.194
so certainly it does contain 668 water molecules.
Thanks,
On Tue, Aug 14, 2012 at 10:13 AM, Peter C. Lai p...@uab.edu wrote:
Did you have waters in the system before adding another 612?
I don't know how VMD counts waters, but another way is to grep -c for SOL in
the resulting
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of
a correct changes?
You are supposed to use the cutoffs appropriate for your forcefield.
Sincerely,
Shima
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of the incorrect value of a new-defined
residue in .rtp file?
Sincerely,
Shima
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in Justin's tutorial ,
323 K is proper, however it was a different system simulated and also many
parameters are not the same as your system . Would you telling me about the
reason of 310 K?
Thanks in advance
Sincerely,
Shima
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Programmer/Analyst | KAUL 752A
Genetics, Div. of Research
On 2012-06-04 05:23:10PM -0400, Justin A. Lemkul wrote:
On 6/4/12 5:16 PM, Shay Teaching wrote:
2012/6/4 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
On 6/4/12 2:59 PM, Shay Teaching wrote:
Dear Gromacs users,
I want to write new analyses
requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
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--
==
Peter C. Lai| University of Alabama-Birmingham
Programmer
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