t true. The -ignh option ignores H atoms in the input
> coordinate file and is useful when there are H atoms with names that do
> not agree with what is specified in the .rtp entry for the given
> residue. The OP's problem is the opposite: the H are not there but need
> to be bu
In your tool.top file the particular lys molecule residue name you
> >> have to modify. Then it will work..Actually grompp can't find the
> molecule
> >> in the topology.
> >>
> >> On Wed 22 Aug, 2018, 11:35 AM Amir Zeb, wrote:
> >>
> >
Hi gromacs users,
I want to simulate a protein where one of the lysine residues is modified
to acetylated lysine and has been denoted by KAC. I want to simulate it by
CharmM 36 ff, but it gave me this error.
Program gmx pdb2gmx, VERSION 5.1.4
Source code file:
/home/chip/Downloads/gromacs-5.1.4/
Hello folks,
Which force field has parameters for S-nitrosoylated cysteine?
How may I get it?
Thanks!
Amir
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I suspect you missed step 5 of
> http://www.gromacs.org/Documentation/How-tos/Adding_
> a_Residue_to_a_Force_Field
>
> pdb2gmx should also have told you things about how many chains, etc. it
> found. What was the full output?
>
> Mark
>
> On Tue, Jan 2, 2018 at 6:52 A
d them.
>
> Mark
>
> On Mon, Jan 1, 2018 at 5:53 AM Amir Zeb wrote:
>
> > Hi gmx users,
> >
> > Wishing you all a very happy new year 2k18.
> >
> > I have modified a particular Tyr residue to phosphorylated Tyr and
> renamed
> > as TP2 per forcef
Thanks Dr. Justin,
Let me try.
~Amir
On Sat, Dec 30, 2017 at 8:14 AM, Justin Lemkul wrote:
>
>
> On 12/30/17 12:23 AM, Amir Zeb wrote:
>
>> Alright Dr. Justin,
>>
>> Is it kindly possible to get CHARMM-compatible parameters for Mn2+ which
>> you haven'
Hi gmx users,
Wishing you all a very happy new year 2k18.
I have modified a particular Tyr residue to phosphorylated Tyr and renamed
as TP2 per forcefield recognizable name. I have used:
gmx pdb2gmx -f xxx.pdb -o xxx.gro -ignh -ter (as full command)
C36m ff
Gromacs v5.0.6
NH3+ as N-terminus
COO-
Alright Dr. Justin,
Is it kindly possible to get CHARMM-compatible parameters for Mn2+ which
you haven't included in the port?
I'm searching the literature too to find something worthy.
Thanks!
~Amir
On Fri, Dec 29, 2017 at 8:17 AM, Justin Lemkul wrote:
>
>
> On 12/29/17
Thanks Dr. Justin.
I didn't add this stuff by my own.
I have created Mn+2 topology by simple pdb2gmx command.
~Amir
On Dec 30, 2017 12:21 AM, "Justin Lemkul" wrote:
>
>
> On 12/29/17 10:11 AM, Amir Zeb wrote:
>
>> Hello dear gromacs users,
>>
>> I
Hello dear gromacs users,
I want to simulate a protein which has two Mn+2 ions as co-factor.
Till the solvation, I could prepare the system, but at neutralization step,
grompp gives me this fatal error.
Fatal error:
Atomtype MN not found
My system has this topology for Mn+2:
[ moleculetype ]
;
particular HIS also read
as HIE by the force filed itself and I should assign them as HIE, because
otherwise I will get the same error as mentioned above.
Thanks for your consideration!
On Mon, Dec 4, 2017 at 6:25 AM, Justin Lemkul wrote:
>
>
> On 12/4/17 1:45 AM, Amir Zeb wrote:
>
>&g
Hello gmx users,
I have generated topology and coordinate files of ZN metalloprotein by
Amber 12 ff. Now I am facing this following issue at grompp run:
"ERROR 1 [file topol_Protein_chain_A.itp, line 49741]:
No default Improper Dih. types"
If I use another ff like Amber99SB- ILDN, there is no
0.
> readline () on closed filehandle IN at distances.pl line 16.
> Use of uninitialized value $ distance in concatenation (.) Or string at
> distances.pl line 30.
> readline () on closed filehandle IN at distances.pl line 16.
> Use of uninitialized value $ distance in concatenati
Solved it,
Thanks every one!
Amir
On Thu, Nov 30, 2017 at 5:06 AM, Justin Lemkul wrote:
>
>
> On 11/30/17 4:04 AM, Rose wrote:
>
>> Till nowi think the only solution is to use gmx distance for each
>> conf.gro files.then use perl script.
>> don't forget to delete gmx distance line from script.
Hello gmx users,
I want to calculate binding free energy for protein-ligand complex by
Umbrella sampling in Gromacs. I have extracted each frame's gro file for
500 frames after pulling simulation. Now, I want to calculate the distances
between the representative gro files by executing the script g
Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 20 November 2017 at 12:34, Amir Zeb wrote:
> > Thanks Mark,
> >
> > Depen
y of the parameterization of the
> metal-protein interactions, for which you would probably need some suitable
> experimental data.
>
> Mark
>
> On Sun, Nov 19, 2017 at 7:48 AM Amir Zeb wrote:
>
> > Hi gromacs users,
> >
> > I want to calculate the energy for
Hi gromacs users,
I want to calculate the energy for comparative analysis of protein with and
without metal ion, wherein I would like to determine the influence of metal
on protein structural stability. I have used gromacs for simulation. Please
suggest me how to do this kind of analysis? Should i
ome/hauren32/Desktop/work/MM_PBSA_2.0/GMXPBSAtool/
> gmxpbsa0-1_TEST.pbs
>
> and the files i have are
> 1. npt.xtc
> 2.npt.tpr
> 2.index.ndx
> 3.topol.top
> 4. gdp.itp
> 5.protein.itp
>
>
>
>
> 2017-08-09 12:22 GMT+08:00 Amir Zeb :
>
> > can you please paste
can you please paste your command line here?
we can judge where you are wrong
On Aug 9, 2017 12:50 PM, "Kingsley Theras Primus Dass ." <
105726...@gms.tcu.edu.tw> wrote:
Hi everyone,
I am trying to calculate the binding free energy between protein and ligand
by using MM/PBSA. I included all the
Hello gmx-users!
I want to simulate a membrane protein, where it sets across the membrane
(means that some of the protein's region lays outside the membrane and is
water exposed). Obviously, the protein will be experiencing two different
environments like membrane and water (heterogeneous conditio
Thanks Justin
Got it, it's working.
On Wed, Aug 2, 2017 at 10:02 AM, Justin Lemkul wrote:
>
>
> On 8/2/17 5:01 AM, Amir Zeb wrote:
>
>> Hello gmx-user
>>
>> I want to simulate a membrane protein with more than one chains like A, B,
>> C etc. I genera
Hello gmx-user
I want to simulate a membrane protein with more than one chains like A, B,
C etc. I generated the strong_posre.itp file as Justing has kindly
explained in his tutorial, and updated the topol.top file by inserting the
same lines. I also updated the minim.mdp file by inserting STRONG
please put this command line
gmx mdrun -v -s xxx.tpr -c xxx.gro -g xxx.log -e xxx.edr -cpi xxx.cpt -o
md_1_0.xtc
good luck
On Wed, Apr 12, 2017 at 10:42 PM, Anshul Lahariya <
anshullahariy...@gmail.com> wrote:
> My md was running. Suddenly power supply was cuts due to some reason and my
> my MD
ssary
> functional groups for FAD are already in CHARMM, just not parametrized
> explicitly, so I suspect a CGenFF topology to be of pretty high quality
> since the analogy will be strong.
>
> -Justin
>
>
>
>> On Friday, March 31, 2017 9:29 AM, Amir Zeb
>> wr
Hello Folks,
I want to simulate a protein where FAD is included as co-factor. I will use
CHARMm36 ff but I don't know the residue ID for FAD in this particular
forcefield. Anyone please let me know by which name FAD is represented in
CHARMm36 ff?
Thanks in advance!
~Amir
--
Gromacs Users mailin
Thanks a lot Das,
You really solved my problem.
Amir
On Mon, Mar 20, 2017 at 3:06 AM, Devashish_Das
wrote:
> Please use this link:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/
>
> On Mon, Mar 20, 2017 at 3:01 PM, Amir Zeb wrote:
>
> > Hello folks,
>
Hello folks,
I want to access the updated discussion on gmx-user list but mostly I'm
getting into this page while searching for "
https://www.mail-archive.com/gmx-users@gromacs.org/index.html";, This page
gives me very early discussion like 2013 and data I could find after 2103.
Please let me know
You probably follow umbrella sampling for free energy calculation.
If it is so, you may change the position of your drug.itp file in topology
file, means that before the protein topology.
I hope this might solve your problem.
Good luck!
Amir
On Thu, Mar 16, 2017 at 2:49 AM, Tasneem Kausar
wrote
Thanks Justin,
Got it
-Amir
On Wed, Mar 8, 2017 at 7:08 PM, Justin Lemkul wrote:
>
>
> On 3/8/17 8:43 PM, Amir Zeb wrote:
>
>> Thanks Justin,
>>
>> The current version I'm working on is 5.0.6, and I don't have access to
>> update this versio
Thanks Justin,
The current version I'm working on is 5.0.6, and I don't have access to
update this version. Can you please let me know how to get files compatible
for this version?
Regards!
-Amir
On Wed, Mar 8, 2017 at 5:32 PM, Justin Lemkul wrote:
>
>
> On 3/8/17 8:11
Hello gmx users,
I want to calculate binding energy for a protein-ligand complex. Obviously,
this is the very first time, I'm handling umbrella sampling, so I faced the
following error.
WARNING 2 [file pull.mdp, line 65]:
Unknown left-hand 'pull_ncoords' in parameter file
WARNING 3 [file pul
Thanks Dr. Justin,
Got it
-Amir
On Fri, Mar 3, 2017 at 5:00 AM, Justin Lemkul wrote:
>
>
> On 3/3/17 1:49 AM, Amir Zeb wrote:
>
>> Hi Dr. Justin,
>>
>> I'm wondering that you have mentioned CHARMm27 is not a valid identifier
>> of
>> protein f
Hi Dr. Justin,
I'm wondering that you have mentioned CHARMm27 is not a valid identifier of
protein forcefield, but we have so many articles already published while
using CHARMm27 ff. Can you please let us know how to trace this
unsuitability of CHARMm27 especially for protein-ligand simulation?
T
Hello gmx-users
I wanted to compute binding free energy for a protein-ligand complex by
gromacs. I sued MM/PBSA approach
http://rashmikumari.github.io/g_mmpbsa/
but here the entropic terms could not be computed which is the backbone
limitation to restrict the actual free energy determination.
P
Thank you Justin,
Got it
Amir
On Sun, Feb 26, 2017 at 7:52 AM, Justin Lemkul wrote:
>
>
> On 2/24/17 1:19 AM, Amir Zeb wrote:
>
>> Hello gmx users,
>>
>> I want to conduct md simulation to explore the comparative stability and
>> interaction mechanism of th
Hello gmx users,
I want to conduct md simulation to explore the comparative stability and
interaction mechanism of the reference compound (experimentally determined)
and the newly screened candidate molecules by virtual screening approach.
The gromacs version 5.0.7 is installed on my cluster. I wa
gt;
> On Thu, Feb 23, 2017 at 1:34 PM, Amir Zeb wrote:
>
> > so what did you find?
> > Did you fix the problem?
> >
> > On Wed, Feb 22, 2017 at 11:51 PM, Subashini .K
> > wrote:
> >
> > > Many tutorials suggest to run two equilibrations and th
means that you didn't produce your simulation run yet?
On Thu, Feb 23, 2017 at 12:06 AM, RAHUL SURESH
wrote:
> I am just doing my production run. I don't get any satisfactory conformer.
>
>
>
> On Thu, Feb 23, 2017 at 1:21 PM, Subashini .K
> wrote:
>
> > Many tutorials suggest to run two equili
so what did you find?
Did you fix the problem?
On Wed, Feb 22, 2017 at 11:51 PM, Subashini .K
wrote:
> Many tutorials suggest to run two equilibrations and then production file.
>
>
> At first, run a restrained equilibrium.
>
>
> Then non-restrained equilibrium followed by production file.
>
>
>
o I dont have traj.xtc file.
>
> On Thu, Feb 23, 2017 at 1:03 PM, RAHUL SURESH
> wrote:
>
> > what is that compact?
> >
> > And my protein is still within the system.(BOX)
> >
> > On Thu, Feb 23, 2017 at 12:40 PM, Amir Zeb wrote:
> >
> >>
:
> using VMD
>
> On Thu, Feb 23, 2017 at 12:32 PM, Amir Zeb wrote:
>
> > how do you visualize your system structure?
> >
> > On Wed, Feb 22, 2017 at 10:58 PM, RAHUL SURESH
> > wrote:
> >
> > > Dear amir
> > >
> > > They are forming long
but again they do deform.
>
>
>
> On Thu, Feb 23, 2017 at 12:26 PM, Amir Zeb wrote:
>
> > Hey
> > I don't know very well about the problem you have.
> > Did you minimize your system well converged?
> > You may go for conjugate minimization
> >
Hey
I don't know very well about the problem you have.
Did you minimize your system well converged?
You may go for conjugate minimization
All the best!
On Wed, Feb 22, 2017 at 10:53 PM, RAHUL SURESH
wrote:
> Simulating a protein with 100residues for 200ns doesn't show any stability.
> There are
Hello Rahul,
Just extend the simulation time in mdp file and repeat the same commands as
you done for early 100 ns.
Best!
On Wed, Feb 22, 2017 at 10:47 PM, RAHUL SURESH
wrote:
> I have a 100ns simulated file.(md.xtc) I need to extend to another 100 ns.
>
> do i need to make any change to mdp f
Hello Abbas,
please suggest
me any solution and also tell me can we use any other forcefield or not?
You may try Amber family forcefields
Residue 97 named ARG of a molecule in the input file was mapped to an entry
in the topology database, but the atom CG used in that entry is not found
in the i
?
Further more, if the case is likely not to flag the -ignh, what might be
the possible consequences?
I trust to listen to your precious negotiation.
Cheers!
Amir
On Tue, Feb 7, 2017 at 12:21 AM, Erik Marklund
wrote:
>
>
> > On 7 Feb 2017, at 08:35, Amir Zeb wrote:
> >
> >
Hello Maria,
f igoring h-atom command is applied ,,then forcefield will ignore all the
added h-atoms
What I know about -ignh flag, it does not mean to remove the h-atoms,
alternatively means that during the topology generation, the force field is
considering the h-atoms as the light atoms and doe
Hello gmx users,
I'm wondering which would be the best force field to create topology for
cobalt. I tried different ff but none of them get the task. I searched the
mailing archive too but I couldn't get the way to solve the issue.
Dr. Justin has just mentioned (https://www.mail-archive.com/gmx
us
Thanks Justin,
I followed your answer on the archive while tracing from researchgate which
you had replayed to a user and solved the problem successfully.
Thanks again.
-Amir
On Tue, Jan 31, 2017 at 5:47 PM, Justin Lemkul wrote:
>
>
> On 1/31/17 7:48 PM, Amir Zeb wrote:
>
>&g
Hello GMX users,
I want to compute the distance between COM of two residues's side chains by
gmx distance option.
When I'm specifying the first group from the selection menu as one residue
and 2nd group as 2nd residue, I'm getting the following error
Inconsistency in user input:
Selection 'A_MT21
Hello gmx users,
I want to measure the distance between the two residues side chains. I will
use the gmx distance to do this. But in the 5.X.X series, I could not find
COM (center of mass) as i want to measure the average point for a side
chain from where I can measure the distance. Can any one pl
I want to simulate ternary complex of protein -DNA -ligand..Is it possible
to simulate it combinely?
Yeah sure, you can, your order might be protein-DNA-ligand during topology
development and gro file format
good luck
On Tue, Jan 24, 2017 at 2:25 AM, maria khan
wrote:
> Dear gromacs Users..
>
Hello every one,
I want to design a simulation system in which water will be used as a
sphere.
I'm not pretty sure how to design the solvent, as a sphere? Obviously,
water will be used as the desired solvent.
Best,
Amir
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* Please search the archive at
http://www.gr
t.sys.kth.se> on behalf of Amir Zeb <
zebami...@gmail.com>
Sent: Thursday, January 19, 2017 12:40 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE
can you please recognize that two extra atoms generated by acepype??
On Jan 19, 2017 4:00 PM, "Subashini .
toms.
>
>
> But, in the top and gro generated by acpype it shows 31 atoms.
>
>
> There lies the problem.
>
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on be
Hello
review the number of atoms in gro file and top file
also check that the 2nd line in gro file showing the total number of atoms
should be in parallel with all the atoms existed in the gro file
this way you may solve the problem
good luck
On Jan 19, 2017 3:20 PM, "Subashini .K" wrote:
> Hi,
Is TYR and SER are N-terminal and C-terminal residues , respectively?
Also, you may compare the corresponding atoms of each residues with same
residues present in your system and does not show the mentioned warning.
All the best
On Fri, Jan 6, 2017 at 10:58 AM, liming_52 wrote:
> Dear Gromacs u
Hello Tasneem,
Same like you, I'm pretty new to this field too. I don't know enough how to
calculate free energy in gromacs. I did only MM/PBSA for binding energy
calculations.
I'll let you know if i get some thing relevant to your question.
All the best.
Thanks
On Thu, Jan 5, 2017 at 10:28 PM,
, "tasneem kausar" wrote:
> Thanks Amir Zeb for your reply
> I have read in literature about the FEPsetup to parametrize the complex
> file (protein+drug) for simulation. This setup builds files based on amber.
> Since I have previously used 54a7ff to simulate the protein a
an 7, 2017 at 10:00 AM, Amir Zeb wrote:
>
> > hello
> > you may use mm/pbsa compiled with gromacs to calculate free energy
> > all the best
> >
> > On Jan 7, 2017 1:27 PM, "tasneem kausar"
> > wrote:
> >
> > > Dear gromacs u
hello
you may use mm/pbsa compiled with gromacs to calculate free energy
all the best
On Jan 7, 2017 1:27 PM, "tasneem kausar" wrote:
> Dear gromacs users
>
> It is first time I am trying to perform free energy calculation of protein
> and drug complex. I am following Justin' s tutorial of mehta
Hello,
According to the best of approach, you may prompt to a list after putting
the concerned command and you should select the desired group number like
one which you have specified for potential energy in you index file.
All the best
Amir
On Thu, Jan 5, 2017 at 12:58 PM, 大木啓輔 wrote:
> Dear
Hello gmx users,
I want gmx clustsize for a protein-ligand complex of 10 ns total run.
I'm getting the error like:
Fatal error:
Lo: 0.0, Mid: 1.0, Hi: 1.0
I don't know how to fix this error?
Regards!
Amir
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http://www.gro
Hi Mijiddorj,
My target protein size is around 250 residues. It's pretty small and i
don't have issue with time. Can you please let me know the actual command
line for cluster analysis?
Regards!
On Thu, Dec 22, 2016 at 12:59 AM, Mijiddorj Batsaikhan <
b.mijidd...@gmail.com> wrote:
> Hi,
>
> Wha
~3-6 nm. Then i superimposed the
input protein structure and the snapshot from the last frame, so the rmsd
was around 5 angstrom between the two structures.
[image: Inline image 1]
On Wed, Dec 21, 2016 at 10:27 PM, Mark Abraham
wrote:
> Hi,
>
> On Thu, Dec 22, 2016 at 5:19 PM Amir Z
ether you need a model with the other parts.
>
> Mark
>
> On Thu, 22 Dec 2016 16:51 Amir Zeb wrote:
>
> > Hello,
> >
> > I have created a homology model for a protein, where the seq. identity
> > between the template and target is 40%. The template structure a
Hello,
You may follow "
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/
"
Everything will go fine
Good luck
Amir
On Wed, Dec 21, 2016 at 8:50 PM, Adarsh V. K.
wrote:
> Dear all,
>
> We have a 419 amino acid long protein and planned Protein-ligand complex MD
> s
Hello,
I have created a homology model for a protein, where the seq. identity
between the template and target is 40%. The template structure also
contains co-factor and an inhibitor in bound form means it is a complex.
I'll have to define the ligand binding site in target (homology model)
based on
alright Mark,
Thanks a lot
On Tue, Dec 20, 2016 at 3:00 AM, Mark Abraham
wrote:
> Hi,
>
> On Tue, Dec 20, 2016 at 9:20 PM Amir Zeb wrote:
>
> > Thanks Mark for your quick response,
> >
> > I did as you mentioned, what i got was actually the total charge of
On Tue, Dec 20, 2016 at 9:12 PM Amir Zeb wrote:
>
> > Hello All,
> >
> > I want to know the total charge carried by a specific residue during or
> > after simulation. Please let me know how may I do it? I don't know the
> > exact command line
> >
> >
Hello All,
I want to know the total charge carried by a specific residue during or
after simulation. Please let me know how may I do it? I don't know the
exact command line
Thanks
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* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-User
thanks to all of you for your advice
amrir
On Mon, Dec 12, 2016 at 4:04 AM, Justin Lemkul wrote:
>
>
> On 12/12/16 2:15 AM, Amir Zeb wrote:
>
>> Hello Surya,
>>
>> I want to simulate a protein where ser is phosphorylated. i used charm26
>> ff
>> but
Hello Mark,
Please help me for this issue
I want to simulate a protein where ser is phosphorylated. i used charm26 ff
but i m getting this error "Atom P in residue SER 4 was not found in rtp
entry SER with 11 atoms
while sorting atoms". can you please suggest me any possible solution for
this iss
sorry, the ff is charm36 and charm26 is miss typed
On Sun, Dec 11, 2016 at 11:15 PM, Amir Zeb wrote:
> Hello Surya,
>
> I want to simulate a protein where ser is phosphorylated. i used charm26
> ff but i m getting this error "Atom P in residue SER 4 was not found in rtp
&g
Hello Surya,
I want to simulate a protein where ser is phosphorylated. i used charm26 ff
but i m getting this error "Atom P in residue SER 4 was not found in rtp
entry SER with 11 atoms
while sorting atoms". can you please suggest me any possible solution for
this issue?
Thanks in advance
Amir
hello mohammad
can you please let me know how to install do_dssp on my gromacs 5.0.6
we have downloaded the package but we could not install
please help
thanks
On Dec 11, 2016 11:45 PM, "Justin Lemkul" wrote:
>
>
> On 12/11/16 1:01 AM, Mohammad Roostaie wrote:
>
>>
>>
>>
>> Hi Gromacs user
hello
go to gro file and find out the atom number from which your concerned
residue starats and ends
copy the atom numbers inbetween and make a separate selection in your index
file for residues and paste therein
you will have the residue number once you prompt by putting hbond
good luck
On Dec 11
Hi
How can I convert xtc file of trajectory to dcd file for dccm analysis?
Thanks
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* For (un)
Hello every one,
I wanna calculate binding energy between protein-ligand complex. I created
all the essential files like .xtc, .tpr, .ndx etc and also did download
pbsa.mdp file. i'm using the command "g_mmpbsa -f mmpbsa.xtc -s md.tpr -n
index.ndx -i pbsa.mdp -pdie 2 -pbsa -decomp" to get xvg as o
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