On 2/14/20 11:13 AM, Andrew Bostick wrote:
Dear gromacs users,
I am doing MD simulation of protein-ligand complex. For ligand, I used
PRODRG server.
My ligand is Tamoxifen (C26H29NO = 57 atoms). I have 3D structure of
Tamoxifen from PDB ID 1YA4 (name of Tamoxifen in this pdb file is CTX). In
Dear gromacs users,
I am doing MD simulation of protein-ligand complex. For ligand, I used
PRODRG server.
My ligand is Tamoxifen (C26H29NO = 57 atoms). I have 3D structure of
Tamoxifen from PDB ID 1YA4 (name of Tamoxifen in this pdb file is CTX). In
PRODRG outputs, ligand is protonated on N atom
On 11/4/19 2:07 AM, Yogesh Sharma wrote:
hello users
I am using ATB server for ligand topology development. there is a section
named FORMAt having options GROMACS, GROMAC11, GROMAC96 and LAMPP what
does it mean? and in files section there is choice for Topology Files and
structure files a
hello users
I am using ATB server for ligand topology development. there is a section
named FORMAt having options GROMACS, GROMAC11, GROMAC96 and LAMPP what
does it mean? and in files section there is choice for Topology Files and
structure files as following
GROMACS G54A7FF All-Atom (ITP fil
hello users
I am using ATB server for ligand topology development. there is a section
named FORMAt having options GROMACS, GROMAC11, GROMAC96 and LAMPP what
does it mean? and in files section there is choice for Topology Files and
structure files as following
GROMACS G54A7FF All-Atom (ITP fil
On 9/25/19 5:46 AM, Pandya, Akash wrote:
Hi,
I have multiple ligand molecules of the same type in my system. If I wanted to
monitor the Cartesian coordinates of each individual ligand during a
simulation, is there a Gromacs tool to do that? or do I have write a custom
script?
You can pri
Hi,
I have multiple ligand molecules of the same type in my system. If I wanted to
monitor the Cartesian coordinates of each individual ligand during a
simulation, is there a Gromacs tool to do that? or do I have write a custom
script?
Some background:
My purpose is to look at binding/unbindin
Hi
The procedure you are following is not ok. Generate the co-ordinate
file of ligand and the topology parameter file. Setup the box and add water
to it. Lastly do energy minimisation.
On Thu 9 May, 2019, 2:33 PM RAHUL SURESH, wrote:
> Hi Users.
>
> I want to simulate ligand in the water box
This will do it (if need particular water model change with cs switch
options, and assumes ligand.gro has the correct final box size)
gmx solvate - cp ligand.gro -cs -o complex.gro
Unless you have a particular number of waters required, then use.:
gmx solvate - cp ligand.gro -cs -o complex.gro -
Hi Users.
I want to simulate ligand in the water box. I prepared a water molecule and
started with pdb2gmx and then planned to follow protein-ligand tutorial.
Unfortunately ended up with an error in gro file format. Have check every
possibility but still couldn't find any solution.
My initial pdb
1/ as long as the frame within the .tpr file or first frame within the .xtc
file fed to trjconv has the molecules/particles as shown in figure 1, then
it should maintain them as such, even if they diffuse away. I'd recheck
what you have done there.
2/ periodic_molecules is for molecules that cros
Hello everyone,
I am trying to simulate interaction of polymer with ligand. The polymer is
represented by infinite sheet build by propagation in 2 dimensions of
monomer obtained from crystal structure. Since the polymer was crystallized
in triclinic unit cell, the propagation of the sheet also app
Sir,
i need to study Crystal complex structure (protein and ligand)
ligand dissociation by using md methods. Is there any way perform in
gromacs like RAMD
if its there means kindly provide tutorial for that it will helpful for me.
Thank You.
Sincerely
S.venkatesh
--
Gromacs Users mail
Hi,
They are presumably looked up from the parameters found normally in the
force field files.
Mark
On Wed, Jan 3, 2018 at 6:22 PM MD wrote:
> Hi Gromacs folks,
>
> I noticed the topology file of ligand from atb site doesn't have dihedral
> angles that include H. Do you know how to create a it
Hi Gromacs folks,
I noticed the topology file of ligand from atb site doesn't have dihedral
angles that include H. Do you know how to create a itp file that has
hydrogen included dihedral parameters?
Thanks,
Ming
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.
Hi Justin
Thank you so much
with best
Farial
From: Justin Lemkul
To: gmx-us...@gromacs.org
Sent: Monday, 14 August 2017, 16:35:58
Subject: Re: [gmx-users] ligand
On 8/14/17 2:03 AM, farial tavakoli wrote:
> Dear Justin
> Thanks for your advice.Now I am trying to cr
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Dear justin
Thank you so much
Yours sincerelyFarial
Sent from Yahoo Mail for iPhone
On Monday, August 14, 2017, 4:35 PM, Ju
On 8/14/17 2:03 AM, farial tavakoli wrote:
Dear Justin
Thanks for your advice.Now I am trying to create a .gro file from the united
atom pdb structure file obtained from ATB by using :editconf -f xxx.pdb -o
xxx.gro
but faced to this warning:
WARNING: all CONECT records are ignored
would
?
thanks alotFarial
From: Justin Lemkul
To: gmx-us...@gromacs.org
Sent: Sunday, 13 August 2017, 21:45:53
Subject: Re: [gmx-users] ligand
On 8/13/17 12:29 PM, farial tavakoli wrote:
> blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
>#715FFA
On 8/13/17 12:29 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; } Dear justin
Thank you for your replyI thought that topology file obtained from A
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Dear justin
Thank you for your replyI thought that topology file obtained from ATB needs to
be changed like PRODRG
Sent from Y
On 8/13/17 3:13 AM, farial tavakoli wrote:
Dear GROMACS users
I noticed my ligand has some broken bonds and changes in atoms arrengement
after md simulation was done. I have read before that no bond is broken and
created in simulation . So why have been ligand changed ?
I think, i have t
Dear GROMACS users
I noticed my ligand has some broken bonds and changes in atoms arrengement
after md simulation was done. I have read before that no bond is broken and
created in simulation . So why have been ligand changed ?
I think, i have to notice that when i wanted to create a ligand top
R99SB for the protein and gaff for ligand? (TIP3P wáter).
> > >>
> > >
> > > GAFF is compatible with AMBER (by design). My comments were warning
> that
> > > one should not use AMBER for a protein in concert with GROMOS for a
> > ligand.
> > >
> > &g
;
> > GAFF is compatible with AMBER (by design). My comments were warning that
> > one should not use AMBER for a protein in concert with GROMOS for a
> ligand.
> >
> > -Justin
> >
> > Best regards.
> >> Lucio Montero.
> >>
> >&
> GAFF is compatible with AMBER (by design). My comments were warning that
> > one should not use AMBER for a protein in concert with GROMOS for a
> ligand.
> >
> > -Justin
> >
> > Best regards.
> >> Lucio Montero.
> >>
> >> Enviado
nd? (TIP3P wáter).
>>
>
> GAFF is compatible with AMBER (by design). My comments were warning that
> one should not use AMBER for a protein in concert with GROMOS for a ligand.
>
> -Justin
>
> Best regards.
>> Lucio Montero.
>>
>> Enviado desde Correo para
a protein in concert with GROMOS for a ligand.
-Justin
Best regards.
Lucio Montero.
Enviado desde Correo para Windows 10
De: Alan
Enviado: martes, 1 de agosto de 2017 11:01 a. m.
Para: Gromacs
Asunto: Re: [gmx-users] ligand topology
Please this GitHub link is totally outdated and not linked
Ok, you should not mix and match forcefields, ¿but in the case of AMBER99SB for
the protein and gaff for ligand? (TIP3P wáter).
Best regards.
Lucio Montero.
Enviado desde Correo para Windows 10
De: Alan
Enviado: martes, 1 de agosto de 2017 11:01 a. m.
Para: Gromacs
Asunto: Re: [gmx-users
Dear Sir
Thank you very much.
On Tue, Aug 1, 2017 at 7:00 AM, Suhaib Shekfeh wrote:
> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
> simply amber ff for small molecules.
> You have to get first amber tools. The last release is amber tools 16
> Get the source code from
Please this GitHub link is totally outdated and not linked in any sense to
the original authors.
Get the correct ACPYPE here:
svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
stable/ccpn/python/acpype acpype
On 1 August 2017 at 15:00, Suhaib Shekfeh wrote:
> Actually, GAFF f
Actually, GAFF forcefield and amber forcefields are compatible. gaff is
simply amber ff for small molecules.
You have to get first amber tools. The last release is amber tools 16
Get the source code from here :
http://ambermd.org/AmberTools16-get.html
after installation you can use antechamber for
Dear Sir
Thank you very much for your reply. Can you give me any link or suggestion
that i can learn for amber force field for protein and ligand.
On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul wrote:
>
>
> On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
>
>> Dear Sir
>>
>> I am new fo
On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
Dear Sir
I am new for protein-ligand complex. I want amber force field (ff03) for my
protein, tip3p for water model and gaff (General Amber force field) for
ligand. I do not know how to produce gaff force field from pdb and then
convert
Dear Sir
I am new for protein-ligand complex. I want amber force field (ff03) for my
protein, tip3p for water model and gaff (General Amber force field) for
ligand. I do not know how to produce gaff force field from pdb and then
convert for gromacs topology.
I have tried ff03 with gromos ligand t
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Dear gromacs users
Is there any way to create ligand topology file by using pdb2gmx instead of
prodrg? Because i use gromos 43a1
On 7/4/17 5:33 AM, Khadija Amine wrote:
Dear gromacs users,
I have a protein with GNP ligand and acetate ACT ion that I want to
simulate.
I have prepared topologies for both GNP and ACT with PRODRG program.
Don't use PRODRG unless you manually reparametrize the charges and charge groups
a
Can anyone help, please?
*Khadija Amine*
Ph.D. Biology and Health
Biochemistry & Bioinformatics
Phone: 9584
On Tue, Jul 4, 2017 at 12:33 PM, Khadija Amine wrote:
> Dear gromacs users,
>
> I have a protein with GNP ligand and acetate ACT ion that I want to
> simulate.
>
> I have prepared t
Dear gromacs users,
I have a protein with GNP ligand and acetate ACT ion that I want to
simulate.
I have prepared topologies for both GNP and ACT with PRODRG program.
My first question is: Where should I exactly include the ACT.itp and
GNP.itp into topol.top file?
My second question is:
I have
On 5/22/17 4:04 AM, abhisek Mondal wrote:
I have used active site residues COM for this time with Ligand COM. As a
test case. r 6-10 | r 78-80 | r 56 | r 63 | r 35 gave me my custom group of
residues belonging to active site. Using both the COMs now I calculated the
vector PL (protein-ligand) a
I have used active site residues COM for this time with Ligand COM. As a
test case. r 6-10 | r 78-80 | r 56 | r 63 | r 35 gave me my custom group of
residues belonging to active site. Using both the COMs now I calculated the
vector PL (protein-ligand) and applied as pull-coord1-vec.
However, I hate
Beg your pardon, I have not ignored your comment entirely regarding using
specific residue COM. I just recently succeeded performing md_umbrella
simulation (using protein COM) on few configurations.
.
I have not used specific residues COM so far as because of some confusions
regrading defining it.
On 5/21/17 9:47 AM, abhisek Mondal wrote:
I did try the code successfully on a configuration generated after pulling.
The NVT approach with direction-periodic geometry worked nicely for the
particular configuration.
However, when I tried to reapply the same code (with modified COMs and thus
pu
I did try the code successfully on a configuration generated after pulling.
The NVT approach with direction-periodic geometry worked nicely for the
particular configuration.
However, when I tried to reapply the same code (with modified COMs and thus
pull_vec) on a different configuration, somethin
On 5/19/17 5:56 AM, abhisek Mondal wrote:
On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul wrote:
On 5/17/17 8:55 AM, abhisek Mondal wrote:
This time I think I got ligand restrained successfully during the umbrella
sampling. I have removed the restrain from protein, as per your advice.
Def
On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul wrote:
>
>
> On 5/17/17 8:55 AM, abhisek Mondal wrote:
>
>> This time I think I got ligand restrained successfully during the umbrella
>> sampling. I have removed the restrain from protein, as per your advice.
>> Defined the COM vector in md_umbrella
On 5/17/17 8:55 AM, abhisek Mondal wrote:
This time I think I got ligand restrained successfully during the umbrella
sampling. I have removed the restrain from protein, as per your advice.
Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
pull_rate1=0.0.
I have uploaded t
This time I think I got ligand restrained successfully during the umbrella
sampling. I have removed the restrain from protein, as per your advice.
Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
pull_rate1=0.0.
I have uploaded the trajectory movie (and other mdp files) in t
On 5/15/17 2:45 AM, abhisek Mondal wrote:
On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul wrote:
On 5/11/17 9:21 AM, abhisek Mondal wrote:
On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal
wrote:
Hi,
Thank you for the explanation. It really cleared some concepts. But I'm
still having m
On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul wrote:
>
>
> On 5/11/17 9:21 AM, abhisek Mondal wrote:
>
>> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal
>> wrote:
>>
>> Hi,
>>>
>>> Thank you for the explanation. It really cleared some concepts. But I'm
>>> still having my ligand moving in thi
On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul wrote:
>
>
> On 5/11/17 9:21 AM, abhisek Mondal wrote:
>
>> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal
>> wrote:
>>
>> Hi,
>>>
>>> Thank you for the explanation. It really cleared some concepts. But I'm
>>> still having my ligand moving in thi
On 5/11/17 1:25 PM, abhisek Mondal wrote:
Alright. I'm trying as per your advice. Actually my system is pretty big
and due to constraint of computation power it is taking me more time to
test vector setup. I really appreciate your time. Thanks a lot for your
suggestions.
One thing I'm worried
Alright. I'm trying as per your advice. Actually my system is pretty big
and due to constraint of computation power it is taking me more time to
test vector setup. I really appreciate your time. Thanks a lot for your
suggestions.
One thing I'm worried about here. In previous mail, I mentioned the
On 5/11/17 9:21 AM, abhisek Mondal wrote:
On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal
wrote:
Hi,
Thank you for the explanation. It really cleared some concepts. But I'm
still having my ligand moving in this step. I have modified the code as:
; Pull code
pull= umbrel
On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal
wrote:
> Hi,
>
> Thank you for the explanation. It really cleared some concepts. But I'm
> still having my ligand moving in this step. I have modified the code as:
> ; Pull code
> pull= umbrella
> pull_ngroups= 1
> p
Hi,
Thank you for the explanation. It really cleared some concepts. But I'm
still having my ligand moving in this step. I have modified the code as:
; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = Protein_chain_A
pull_group1 = ACO
pu
On 5/8/17 10:00 AM, abhisek Mondal wrote:
On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul wrote:
On 5/7/17 1:57 AM, abhisek Mondal wrote:
Hi,
For your ease of understanding regarding what is happening during this
above said umbrella-mdrun, I have shared the trajectory video file the
foll
On 5/8/17 9:04 AM, Pedro Fernandes wrote:
Good afternoon,
I’m trying to do molecular dynamics (protein-ligand) with a ligand that has a
boron atom.
Can anyone help me or give me some information how can I do the
parameterization of the ligand.
The details will depend on the force field yo
On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul wrote:
>
>
> On 5/7/17 1:57 AM, abhisek Mondal wrote:
>
>> Hi,
>>
>> For your ease of understanding regarding what is happening during this
>> above said umbrella-mdrun, I have shared the trajectory video file the
>> following link.
>> https://drive.
Good afternoon,
I’m trying to do molecular dynamics (protein-ligand) with a ligand that has a
boron atom.
Can anyone help me or give me some information how can I do the
parameterization of the ligand.
Best Regards,
Pedro Fernandes
--
Gromacs Users mailing list
* Please search the archive at
On 5/7/17 2:22 PM, abhisek Mondal wrote:
Hello Justin,
Thank you for the explanation. I'm really new to the field so choosing
factors in a bit confusion.
You said in this set up the ligand can still move around X and Y direction.
My question is what if I set pull_k1=0? The ligand also won't mo
Hello Justin,
Thank you for the explanation. I'm really new to the field so choosing
factors in a bit confusion.
You said in this set up the ligand can still move around X and Y direction.
My question is what if I set pull_k1=0? The ligand also won't move this
way.
You mentioned that during this r
On 5/7/17 1:57 AM, abhisek Mondal wrote:
Hi,
For your ease of understanding regarding what is happening during this
above said umbrella-mdrun, I have shared the trajectory video file the
following link.
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
Is this normal given t
Hi,
For your ease of understanding regarding what is happening during this
above said umbrella-mdrun, I have shared the trajectory video file the
following link.
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
Is this normal given that the mdp code being used ? I basically hav
Hi,
I have completed pulling as per the tutorial stated. But having a strange
issue during umbrella sampling. When I execute:
*mpirun -np 320 /app/gromacs462/bin/mdrun_mpi -v -deffnm umbrella8 -pf
pullf-umbrella8.xvg -px pullx-umbrella8.xvg*
The gro file generated at the end shows the ligand is wa
Hi,
On Wed, 5 Apr 2017 08:49 RAHUL SURESH wrote:
> for Command
>
>
>
> *gmx grompp -f em.mdp -c solv.gro -p conformer.top -o ions.tpr*
> I get the following error.
>
>
> *Warning: atom name 5839 in conformer.top and solv.gro does not match (H81
> - 1H8)Warning: atom name 5840 in conformer.top an
Check the total number of atoms at the top of topology files. If you have
made a complex manually then the numbers had to be accounted for.
On Wed, Apr 5, 2017 at 12:18 PM, RAHUL SURESH
wrote:
> for Command
>
>
>
> *gmx grompp -f em.mdp -c solv.gro -p conformer.top -o ions.tpr*
> I get the follo
for Command
*gmx grompp -f em.mdp -c solv.gro -p conformer.top -o ions.tpr*
I get the following error.
*Warning: atom name 5839 in conformer.top and solv.gro does not match (H81
- 1H8)Warning: atom name 5840 in conformer.top and solv.gro does not match
(H82 - 2H8)*
Is it really an issue or ca
Hi,
The run will be slightly slower with the restraints. But more significant
will be the further equilibration time to start to sample the unrestrained
ensemble.
Mark
On Thu, 30 Mar 2017 12:26 RAHUL SURESH wrote:
> I am running NVT Equilibration for Protein_ligand complex as per the the
> tut
I am running NVT Equilibration for Protein_ligand complex as per the the
tutorial.
Will time consumption for equilibration increase in applying position
restrains for both ligand and protein?
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
--
Gromacs Users m
I’m using MM-PBSA on gromacs to calculate free binding energy of some
ligands into K-Ras (pdb-ID: 4epy). To validate MD simulation protocol and
to setup a rational threshold for evaluating the results, the co-crystal
ligand was considered as the reference ligand. Results showed that free
binding en
On 7/6/16 12:26 PM, Chetan Puri wrote:
I am confused with the fact that after processing ligand through prodrg
whatever pdb file you get it doesn't show aromatic ring double bonds( if we
view it using pymol or vmd)
And I don't understand that although it shows aromatic ring planar but no
double
I am confused with the fact that after processing ligand through prodrg
whatever pdb file you get it doesn't show aromatic ring double bonds( if we
view it using pymol or vmd)
And I don't understand that although it shows aromatic ring planar but no
double bonds are present.
So is it the way aromat
Use ATB for sure. PRODRG co-ordinates, charges are highly doubtful. I have
prepared my ligand's topology using PRODRG and it took me almost 10 days to
correct the charges. ATB is pretty good.
Sent from my iPhone
> On 05-Jul-2016, at 10:26 pm, Justin Lemkul wrote:
>
>
>
>> On 7/5/16 10:50 A
On 7/5/16 10:50 AM, Chetan Puri wrote:
I am trying to do a protein- ligand simulation.
And the prodrg server provides the ligand out put by completely removing
the double bonds(making it saturated)
So is there any way to do it.
See the PRODRG FAQ for dealing with incorrect protonation. T
I am trying to do a protein- ligand simulation.
And the prodrg server provides the ligand out put by completely removing
the double bonds(making it saturated)
So is there any way to do it.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_List
>> Dear Justin and Nikhil,
>>
>> Many thanks for your suggestions. Justin, I had optimized the parameters
>> using VMD's FFTK toolkit, so I just replaced my results in the *.str file
>> obtained from paramchem.
>>
>> I tried minimizing the ligand in vaccum and in a solvent box, in both
>> cases, th
On 3/25/16 8:03 PM, Soumya Lipsa Rath wrote:
Dear Justin and Nikhil,
Many thanks for your suggestions. Justin, I had optimized the parameters
using VMD's FFTK toolkit, so I just replaced my results in the *.str file
obtained from paramchem.
I tried minimizing the ligand in vaccum and in a sol
Dear Justin and Nikhil,
Many thanks for your suggestions. Justin, I had optimized the parameters
using VMD's FFTK toolkit, so I just replaced my results in the *.str file
obtained from paramchem.
I tried minimizing the ligand in vaccum and in a solvent box, in both
cases, the molecule just scatte
On 3/25/16 9:33 AM, Nikhil Maroli wrote:
Dear justin,
if the topology is bad how bonds will break in MD? am i missing anything
The bonds don't break. The OP was presumably using some imprecise language to
describe a badly distorted structure.
-Justin
--
=
Dear justin,
if the topology is bad how bonds will break in MD? am i missing anything
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For
On 3/24/16 8:35 PM, Soumya Lipsa Rath wrote:
Dear gromacs users,
I have a protein-ligand system to simulate. I got the parameters from
CHARMM CGENFF and converted it to gromacs compatible parameters using
"cgenff_charmm2gmx.py" script as Justin had suggested previously.
Following the Protein-l
Soumya Lipsa Rath writes:
>
> Dear gromacs users,
>
> I have a protein-ligand system to simulate. I got the parameters from
> CHARMM CGENFF and converted it to gromacs compatible parameters using
> "cgenff_charmm2gmx.py" script as Justin had suggested previously.
> Following the Protein-ligand
Dear gromacs users,
I have a protein-ligand system to simulate. I got the parameters from
CHARMM CGENFF and converted it to gromacs compatible parameters using
"cgenff_charmm2gmx.py" script as Justin had suggested previously.
Following the Protein-ligand tutorial of gromacs closely, I included the
Can somebody suggest what could be the best possible way for generating
small molecules topology file and charge determination ( OPLS force field)
as I want carry out a simulation for miscell formation between small
ligands.
--
Gromacs Users mailing list
* Please search the archive at
http://www
Dear GMX users,
I am trying to generate a custom virtual site for a C-NH3 group of a
ligand.
As a first test, I would like to use the parameters of the Lys virtual
site, but I can't see how the coordinates of the dummy atoms are generated
(I have already checked the tutorial and the gromacs manual)
Hi,
At least for some definitions of contacts, you can get what you want with
suitable use of gmx select. With a suitable selection that selects residues
that you consider to be in contact, and depending on what you want, -on,
-om, or -of should give you something useful.
Best regards,
Teemu
On
Hello:
I would like to calculate which residues does my ligand contact with
during the MD simulation. I am just wondering is there any module for
calculating ligand contact map?
Thank you very much
Albert
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/S
On 5/21/15 4:51 PM, Ebert Maximilian wrote:
Thanks for your comment and sorry for my weird english. I must have been in my
thoughts :).
I was also wondering if I attach covalently a protein to another protein or a
large organic molecule through a residue in the middle of the sequence my
app
Thanks for your comment and sorry for my weird english. I must have been in my
thoughts :).
I was also wondering if I attach covalently a protein to another protein or a
large organic molecule through a residue in the middle of the sequence my
approach would not work. Does anyone have a suggest
On 5/21/15 4:30 PM, Ebert Maximilian wrote:
Hi there,
I am about to setup a protein ligand complex in which the the amino acid is
covalently bound to the ligand. What I was about to do is to build an
artificial amino acid (in this case serine) with the ligand attached to it an
derive partia
Hi there,
I am about to setup a protein ligand complex in which the the amino acid is
covalently bound to the ligand. What I was about to do is to build an
artificial amino acid (in this case serine) with the ligand attached to it an
derive partial charges using antechamber or the RED server. T
On 1/27/15 3:41 AM, neha bharti wrote:
Hello All
I am performing Molecular dynamics simulation of protein and ligand
complex. I am using GROMOS96 53a6 force field. For Ligand topology file I
am using Automated topology builder.
In the grompp step ( grompp -f ion.mdp -c solv.gro -p topol.top -o
Hello All
I am performing Molecular dynamics simulation of protein and ligand
complex. I am using GROMOS96 53a6 force field. For Ligand topology file I
am using Automated topology builder.
In the grompp step ( grompp -f ion.mdp -c solv.gro -p topol.top -o
ions.tpr) when I tried to add ion it gives
On 12/2/14 6:00 AM, RINU KHATTRI wrote:
hello gromacs users
i am working on complex with popc membrane
i am facing the problem -- ligand is not attached in the protein
i am following the previous mail protocol
and pasted the ligand in final system_shrink.gro file after this i saw
the .gro file
hello gromacs users
i am working on complex with popc membrane
i am facing the problem -- ligand is not attached in the protein
i am following the previous mail protocol
and pasted the ligand in final system_shrink.gro file after this i saw
the .gro file in vmd ligand is very distant to protein it
On 11/12/14 5:10 AM, md kashif wrote:
Dear all
The protein+ligand complex energy is -1.05e+06 and energy of protein
only(without docking) is -1.5...e+06, what does it mean?
It means that you have two systems with two different energies. In order to
dock the ligand, you must have start
Dear all
The protein+ligand complex energy is -1.05e+06 and energy of protein
only(without docking) is -1.5...e+06, what does it mean?
On Wed, Nov 12, 2014 at 9:57 AM, md kashif
wrote:
> Hello everyone
> please suggest me that is there any change in protein energy after docking
> the ligand
Dear md kashif,
my protein energy is
-1.5e+06 and now after docking with ligand it becomes -1.05e+06.
what does it mean?
is it is the energy of ligand_protein complex or simply the protein???
In docking generally the receptor is rigid, then why the receptor will
change its energy ?? the
Hello everyone
please suggest me that is there any change in protein energy after docking
the ligand to my energy minimized protein? my protein energy is
-1.5e+06 and now after docking with ligand it becomes -1.05e+06.
what does it mean?
Thanks
--
Gromacs Users mailing list
* Please sea
1 - 100 of 128 matches
Mail list logo
