Dear GROMACS users
I need to run a MD on my Protein-peptide ligand complex in GROMACS. I generated
my ligand topology by gromose96 54a7 ff ( [moleculetypes] was Protein_chain_B)
and converted it to .itp file to string it in Protein.top file, then, added
Protein_chain_B in [ molecules ] directive
Hi,
I think the 1070s and 1080s are the best value for money. These days, given
that it's I think it costs ~20% more, the 1080 is probably a bit better
value for money, but it's going to be a bit above $500, I think.
Also note that we're working on new GPU acceleration-related features that
will
On 10/2/17 11:14 PM, Dallas Warren wrote:
Thanks for the reply Justin.
I am just going to use the largest exclusion bond distance I can, then
ignore the RDF of those beyond that distance.
Seems curious to me (not actually understanding what grommp is
generating) that the list is so large. Th
On 10/3/17 4:26 AM, farial tavakoli wrote:
Dear GROMACS users
I need to run a MD on my Protein-peptide ligand complex in GROMACS. I generated
my ligand topology by gromose96 54a7 ff ( [moleculetypes] was Protein_chain_B)
and converted it to .itp file to string it in Protein.top file, then
On 10/3/17 9:17 AM, farial tavakoli wrote:
Dear Justin
Thank you so much for your reply.
You mean , I should generate a topology file for my complex instead of
creating topology for each of them separately ?
As long as the protein and peptide ligand are denoted as being in
separate c
Hi, I was wondering what the best approach is to simulate a negatively charged
topology imported from ANTECHAMBER (which can't do integral charges):
1. Do QM calculations on the molecule, then edit the output from Antechamber
or
2. Do something else.
Sergio Manzetti
[ http://www.fjordfor
Hi!
If your goal is to generate the atomic partial charges for a new
residue/molecule (not existing in the FF you are interested in using), then
doing the QM calculations is a must in most cases. For example, AMBER FFs
have a well documented and specific recipe you can easily follow, which
involve
Thanks Joao, I am on the way with the QM part, but making the topology for GMX
is a little bit more complicated. I thought of generating one with ANTECHAMBER
Of a neutral species, then edit the topology itp file manually, but the propers
are quite complex to re-edit.
How did you get around thi
I just left work and I'm terrible with typing on the phone, so please bear
with me.
Since I mostly work with proteins and modified residues it was always worth
it for me to edit the actual FF instead of making an itp by hand. This way
I let pdb2gmx do the tedious work of building the topology for
Thanks, in which file do you add your residue, do you have an example?
Thanks!
Sergio Manzetti
[ http://www.fjordforsk.no/logo_hr2.jpg ]
[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ h
This can potetially involve minimal editting or a lot of work. If you will
be using atom types already in place, you mainly need to edit the rtp file.
The charges, bonds and impropers go there. Other files need minimal work
like the residuetypes.dat and possibly the hdb, r2b, etc.
Avoid touching t
HI
It is quite easy to derive RESP charges and use them with GROMACS. You could
follow the steps
1) Build a pdb file of your molecule/modified residue
2) Use the web server pyRED
(http://upjv.q4md-forcefieldtools.org/REDServer-Development/) and derive the
RESP charges. The webserver will al
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Thanks alot for your advxe
I would really appreciate if you advice me more to split protein and ligand in
index file, I saw the
Hi,
I'm sure we have opportunities to improve this code - please do file a
redmine issue with repro inputs so we can profile and see!
Thanks,
Mark
On Tue, Oct 3, 2017 at 3:05 PM Justin Lemkul wrote:
>
>
> On 10/2/17 11:14 PM, Dallas Warren wrote:
> > Thanks for the reply Justin.
> >
> > I am
Or this... :) I've never used it, but I'm sure it works like a charm. I
personally prefer to be more involved in all stages of the process, but I'm
a bit old school and I like to avoid "black boxes" for my own learning
benefit. That being said, I'm sure it does the job and it's faster &
simpler. It
dear gmx-users,
my simulation has been running for sometime but now I want to know how long is
left for the simulation to be completed. I need help with the command to
analyse a running simulation.
Best regards,
Bukunmi
--
Gromacs Users mailing list
* Please search the archive at
http://www.g
On 10/3/17 11:13 AM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Thanks alot for your advxe
I would really appreciate if you advice me more to sp
On 10/3/17 12:03 PM, Bukunmi Akinwunmi wrote:
dear gmx-users,
my simulation has been running for sometime but now I want to know how long is
left for the simulation to be completed. I need help with the command to
analyse a running simulation.
The -v option of mdrun prints a running estima
see gmx check -h option
On 3 Oct 2017 21:33, "Bukunmi Akinwunmi" wrote:
> dear gmx-users,
> my simulation has been running for sometime but now I want to know how
> long is left for the simulation to be completed. I need help with the
> command to analyse a running simulation.
>
> Best regards,
> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
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> or, via email, send a message with subject or body 'h
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } So how should I split protein and ligand from each other to
create .mdp files?
Sent from Yahoo Mail for iPhone
On Tuesday,
On 10/3/17 1:08 PM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } So how should I split protein and ligand from each other to
create .mdp files?
Hi, is there a tutorial for importing fully charged non-peptid topologies for
the AMBER FF ISBN type to GMX somewhere ?
Thanks
Sergio Manzetti
Fjordforsk AS
Midtun
6894 VangsnesNorge
Org.nr. 911 659 654
Tlf: +47 57695621Økolab | Nanofactory | A
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Oh I am sorry. Yes I am trying to run md on my protein peptide
complex. At first you advice me to use pdb2gmx to generate a topo
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Because in tuturial , energygroups = protein JZ4So I think ,I
have to seperate my ligand and Protein in .mdp files and determine
Hi,
In addition to my previous email
If you have all the parameters obtained from RESP and tleap program (mol2,
frcmod and lib) you could use the ACPYPE program to obtain the itp file for
GROMACS
See
http://www.shourjya.thinkbiosolution.com/assigning-point-charges-to-non-standard-molecules
Thanks, this is very useful! I was looking at the 1080 and the pricing
is fairly acceptable.
Will keep in mind about CR version. Actually, we wouldn't be buying
anything except for the GPUs. It seems like a colleague of ours is
unhappy with the performance of his Xeon-based workstation and we
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