hi i am working of protein ligand binding free energy calculation, i have seen
some tutorials, like from alchemistry websites and from some paper works. i
made ligand topology with acpype (amber.ff) and used pdb2gmx for protein
topology, then i combined gro files to make a complex. now i dont kn
Hii
I am simulating protein (PfCDPK5) in water. After performing energy
minimization, the potential energy of my protein is 2.86082e+07. As
mentioned in the tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html,
the Epot should be negative.
The em.mdp
Thanks! It solved most of the problem.
I am now getting an error during energy minimization:
The [molecules] section of your topology specifies more than one block of
a [moleculetype] with a [settles] block. Only one such is allowed. If you
are trying to partition your solvent into different *grou
On 2/17/16 5:41 PM, Irem Altan wrote:
Hi,
I would like to use TIP4P2005 with Gromacs 4.6.5 for a protein simulation with
water. I have the .itp and .gro files for the model.
I am using a slightly modified version of the Amber forcefields, so I have a
folder called amber99sb.ff in my working
Thanks Justin,
I think that¹s everything I need to know.
Kind regards
Anthony
Dr Anthony Nash
Department of Chemistry
University College London
On 17/02/2016 22:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Justin Lemkul"
wrote:
>
>
>On 2/17/16 5:11 PM, Nash, Anthony
Hi,
I would like to use TIP4P2005 with Gromacs 4.6.5 for a protein simulation with
water. I have the .itp and .gro files for the model.
I am using a slightly modified version of the Amber forcefields, so I have a
folder called amber99sb.ff in my working directory. I have added a file called
tip
On 2/17/16 5:11 PM, Nash, Anthony wrote:
Hi,
Thanks for the information, Mark. I fully parameterised the bonded terms
using QM data and some software I wrote. Now that I’ve sorted out
ffnonbonded [atomtypes], all that remains are some missing angle terms. I
want to have the forcefield files co
Hi,
Thanks for the information, Mark. I fully parameterised the bonded terms
using QM data and some software I wrote. Now that I’ve sorted out
ffnonbonded [atomtypes], all that remains are some missing angle terms. I
want to have the forcefield files correct so an MD simulation can be
generated wi
Hi,
Your MOD residues are LYS connected by a ring, so the atom types and bonds
sections should be pretty much as for LYS, with the ring parts perhaps
along the lines of TYR. If you have done a full parameterization somehow
and have specialized atom types, then yes, those bonded and non-bonded
para
Dear Mark,
I didn’t expect the problem was in ffnonbonded.itp. Problem solved. Thanks
for the earlier hint.
Anthony
On 17/02/2016 18:01, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Nash, Anthony"
wrote:
>Hi Mark,
>
>Further to my earlier email. I’ve answered the query as
Hello,
Using the flag -DGMX_USE_TNG=off does not help.
Scanning dependencies of target gmx
[ 98%] Building CXX object share/template/CMakeFiles/template.dir/template.cpp.o
[100%] Building CXX object src/programs/CMakeFiles/gmx.dir/gmx.cpp.o
[100%] Building CXX object src/programs/CMakeFiles/gm
Hi Mark,
Further to my earlier email. I’ve answered the query as to whether atom
types and names can be the same. This is fine, judging by The N N and O O
in all of the amino acid types.
I suspect I either have an additional problem or I have identified the
root cause of my original problem. Ever
Hi Mark,
Thanks for the reply. I’m a little confused when you say “Choose existing
types”. Are you saying that I am confined to only those atom types that
come along with the forcefield upon installation, or that I can add new
types but I’ve made a slight mishap between when specifying them within
As soon as I sent this off I realized that the work you refer to is
probably the one that was done by/at DE Shaw, so they must have used
Desmond so the non-bonded treatment is not exactly as in AMBER, but my
point is still valid regarding trying to reproduce the pair list
buffer.
--
Szilárd
On We
Hi,
The short-range interaction treatment in AMBER and GROMACS is quite
different (to the best of my knowledge), so obsessing about rlist
seems pointless to me.
AMBER uses a heuristic list update where search is triggered based
particles tracking ("safe" but inefficient strategy), whereas GROMACS
thank you Justin,
kind as always!
I hope that David (or who knows gmx chi better) will have a look at this
post soon.
In the meanwhile I'll use gmx chi (5.0.4), having care of keeping an eye on
the results , and comparing them with other source.
Regards,
Francesco
On 17 February 2016 at 12:49,
Hi,
You've specified a type for your atom in [atoms] and elsewhere a bond that
uses it. Grompp has to find parameters for a bond between those two types,
etc. Choose existing types ;-)
Mark
On Wed, 17 Feb 2016 17:27 Nash, Anthony wrote:
> Hi all,
>
> As per a previous email (cross linking two
Hi all,
As per a previous email (cross linking two peptide chains), I¹ve created a
brand new crosslink (think disulphide bond) residue from scratch. I have
defined it in all the files necessary (.rtp, residuetypes, specbond,
atomtypes, ffbonded, ffnonbonded) and it has got past pdb2gmx with no
pro
Hi,
Yes, what you say is true, but very much "in short" and AFAIK true of all
MD packages. :-)
If e.g. AMBER (or anyone else) has a test suite for any force field, then
we'll seriously consider implementing it, to e.g. verify before each
release. :-) IMO, defining such a suite is a research topic
Hey :)
Since pressure is so ill-defined at those volumes, you may as well run NVT
then at a more or less plausible volume. That will relieve the worry that
the deviations from the intended physics (in light of the force field
chosen) will cause the system to expand or contract out of control and y
On 2/17/16 7:11 AM, Francesco Carbone wrote:
Thank you Justin,
I'm not a pro in C, but I think that in the code, the omega angle is
defined as CA-C-N-CA (Bug #953 discussed this)
...
dl[i].j0[edOmega] = n/4;
id[n++] = dl[i].atm.minCalpha;
id[n++] = dl[i].atm.minCalpha;
id[n++] = dl[i].atm.N;
i
maybe just a historical curiosity, but small systems with only 100
molecules or so and cutoffs of 0.7 nm were considered as best practices,
maybe even state-of-art, in computer simulations of liquids:
J. Chem. Phys. 79, 926 (1983); http://dx.doi.org/10.1063/1.445869
nowadays you have to use syste
Thank you Justin,
I'm not a pro in C, but I think that in the code, the omega angle is
defined as CA-C-N-CA (Bug #953 discussed this)
...
dl[i].j0[edOmega] = n/4;
id[n++] = dl[i].atm.minCalpha;
id[n++] = dl[i].atm.minCalpha;
id[n++] = dl[i].atm.N;
id[n++] = dl[i].atm.Cn[1];
...
I then calculated
In short, FFs were tested to some degree when they were added in GROMACS
to reproduce AMBER results, but there is no certainty if they actually
do this now and 'correct' mdp settings to run them are unknown. For any
of the versions that are listed in GROMACS.
Is that correct, or I'm missing som
you are on the right way.
set high pressure.
set cut-offs to half box side.
run classical MD, ~10 000 steps, and, afterwards, manually increase the box
sides to mimic the experimental density
in the plane-wave DFT, run local optimization prior to AIMD.
On Tue, Feb 16, 2016 at 4:01 PM, M
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