[gmx-users] query

[amir zeb]

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 output file, but
i am getting comment like "Illegal instruction (core dumped)". I am using
gromacs version 5.0.6
can anyone please help me out?

regards!
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[gmx-users] Inconsistency in user group

[Amir Zeb]

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_MT218' does not evaluate into an even number of positions
(there
are 11 positions)

Can anyone please help me for possible solution of this issue?

Thanks in advance!
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Re: [gmx-users] Inconsistency in user group

[Amir Zeb]

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 <jalem...@vt.edu> wrote:

>
>
> On 1/31/17 7:48 PM, Amir Zeb wrote:
>
>> 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_MT218' does not evaluate into an even number of positions
>> (there
>> are 11 positions)
>>
>> Can anyone please help me for possible solution of this issue?
>>
>>
> You'll need to provide your exact command and any relevant screen output.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Ignoring H-atoms.

[Amir Zeb]

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 does not pay much attention
to consider their parameters so accurately.

it would be a vaccum simulation if
the h-atom will be ignored

Also, in case of vacuum simulation, I think there is no water addition,
while here we are gonna adding the water during the salvation step  of the
procedure. So, I think you don't need to worry about it.

At the end, I would like to appraise in deep the explanation of other users.

Cheers!

Amir

On Mon, Feb 6, 2017 at 10:12 PM, maria khan 
wrote:

> Dear Gromacs users,,
>
> if igoring h-atom command is applied ,,then forcefield will ignore all the
> added h-atoms,,,so my question is then it would be a vaccum simulation if
> the h-atom will be ignored,,secondly the results will be also differnt then
> when h-atoms are considered.
>
> Regards..
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Re: [gmx-users] Ignoring H-atoms.

[Amir Zeb]

Thanks Erik,

I got the explanation you kindly posted regarding the posted discussion.

I would like to extend the question that if some one does not flag the
-ignh, so does it mean that the input H-atoms are still there and the force
field will consider them during the rtp file generation?
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 <erik.markl...@kemi.uu.se>
wrote:

>
>
> > On 7 Feb 2017, at 08:35, Amir Zeb <zebami...@gmail.com> 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 does not pay much
> attention
> > to consider their parameters so accurately.
>
> No. -ignh ignores the hydrogen atoms in the input structure, but uses the
> rtp file(s) to generate new hydrogens. This is useful, for example, when
> some hydrogens are missing in the pdb file. The structure and topology will
> therefore contain hydrogens in the end also with -ignh.
>
> Kind regards,
> Erik
>
> >
> > it would be a vaccum simulation if
> > the h-atom will be ignored
> >
> > Also, in case of vacuum simulation, I think there is no water addition,
> > while here we are gonna adding the water during the salvation step  of
> the
> > procedure. So, I think you don't need to worry about it.
> >
> > At the end, I would like to appraise in deep the explanation of other
> users.
> >
> > Cheers!
> >
> > Amir
> >
> > On Mon, Feb 6, 2017 at 10:12 PM, maria khan <mariabiochemi...@gmail.com>
> > wrote:
> >
> >> Dear Gromacs users,,
> >>
> >> if igoring h-atom command is applied ,,then forcefield will ignore all
> the
> >> added h-atoms,,,so my question is then it would be a vaccum simulation
> if
> >> the h-atom will be ignored,,secondly the results will be also differnt
> then
> >> when h-atoms are considered.
> >>
> >> Regards..
> >> --
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[gmx-users] Force field for Cobalt topology??

[Amir Zeb]

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...@gromacs.org/msg46374.html) that there is no such suitable force field
yet to deal with transition metals correctly due to their lack of fixed
charge. But this was commented so back.
Let me know if the recent advances had solved such issue.

Regards!

Amir
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[gmx-users] water sphere formation

[Amir Zeb]

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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Re: [gmx-users] simulation of ternary complex

[Amir Zeb]

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..
>
> I want to simulate ternary complex of protein -DNA -ligand..Is it possible
> to simulate it combinely?
>
> secondly..Gromacs has no graphical interface to visualize results..how can
> we resolve this issue..Using VMD i have some issues regarding
> trajectories..
>
> Regards..
>
> Maria khan.
>
> ICS,,university of peshawar..
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[gmx-users] Side chain distance

[Amir Zeb]

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 please let me know
the full command line how to measure the distance between the two COMs for
side chains?

Thanks in deep!
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[gmx-users] Protein and Ligand position restraint

[Amir Zeb]

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 want to listen to
your suggestions regarding:

1. Is it rational to restraint the position of the protein and/or ligand?
2. If position restraint is necessary, which part of the system should I
restraint?
3. Also, at which steps, I may restraint them, means NVT, NPT and md
production? Because the Justin tutorial mentioned the release of restraint
immediately after equilibration steps.

I have co-factor FAD as the essential part of the protein, so I would like
to consider protein-FAD as single moiety. I searched from gmx-user archive
and Justin Tutorial, but I could not get a sound proof for this dilemma.

Hope to listen to you soon

Thanks

Amir
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Re: [gmx-users] deformation in simulation

[Amir Zeb]

Hello,

You would have xxx.xtc file. actually, this is your xtc file what ever the
name you have given, just put your corresponding xtc file therein.
Once you are directed to prompt option, you should select 0 "system"



On Wed, Feb 22, 2017 at 11:39 PM, RAHUL SURESH <drrahulsur...@gmail.com>
wrote:

> Also I dont have traj.xtc file.
>
> On Thu, Feb 23, 2017 at 1:03 PM, RAHUL SURESH <drrahulsur...@gmail.com>
> 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 <zebami...@gmail.com> wrote:
> >
> >> alright
> >> you first centralize your system by the following command
> >> trjconv -f traj.xtc -s md.tpr -n index.ndx -o md.xtc -pbc mol -ur
> compact
> >> and then visualize
> >> probably you would have solved it. This is some how visualization
> >> problem.
> >>
> >> On Wed, Feb 22, 2017 at 11:06 PM, RAHUL SURESH <drrahulsur...@gmail.com
> >
> >> wrote:
> >>
> >> > using VMD
> >> >
> >> > On Thu, Feb 23, 2017 at 12:32 PM, Amir Zeb <zebami...@gmail.com>
> wrote:
> >> >
> >> > > how do you visualize your system structure?
> >> > >
> >> > > On Wed, Feb 22, 2017 at 10:58 PM, RAHUL SURESH <
> >> drrahulsur...@gmail.com>
> >> > > wrote:
> >> > >
> >> > > > Dear amir
> >> > > >
> >> > > > They are forming long bonds. I hope you understand what i mean.
> Like
> >> > few
> >> > > > molecules move away from the protein still bonded. and they again
> >> > > converge
> >> > > > at some point but again they do deform.
> >> > > >
> >> > > >
> >> > > >
> >> > > > On Thu, Feb 23, 2017 at 12:26 PM, Amir Zeb <zebami...@gmail.com>
> >> > 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
> >> > > > >
> >> > > > > All the best!
> >> > > > >
> >> > > > > On Wed, Feb 22, 2017 at 10:53 PM, RAHUL SURESH <
> >> > > drrahulsur...@gmail.com>
> >> > > > > wrote:
> >> > > > >
> >> > > > > > Simulating a protein with 100residues for 200ns doesn't show
> any
> >> > > > > stability.
> >> > > > > > There are some deformation(long-bonds) in the structure
> >> throughout
> >> > > the
> >> > > > > > process. Why is that so? Can I choose any stable structure in
> >> > between
> >> > > > > these
> >> > > > > > 200ns, for example say 176ns. Or is there any other way to
> make
> >> > them
> >> > > > work
> >> > > > > > good.I need your valuable suggestions
> >> > > > > >
> >> > > > > > --
> >> > > > > > *Regards,*
> >> > > > > > *Rahul Suresh*
> >> > > > > > *Research Scholar*
> >> > > > > > *Bharathiar University*
> >> > > > > > *Coimbatore*
> >> > > > > > --
> >> > > > > > Gromacs Users mailing list
> >> > > > > >
> >> > > > > > * Please search the archive at http://www.gromacs.org/
> >> > > > > > Support/Mailing_Lists/GMX-Users_List before posting!
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> >> > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx
> >> -users
> >> > > or
> >> > > > > > send a mail to gmx-users-requ...@gromacs.org.
> >> > > > > >
> >> > > > > --
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> >> > > 

Re: [gmx-users] deformation in simulation

[Amir Zeb]

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.
>
>
> Do not know the aim of your simulations.
>
>
> Hope this answer helps.
>
>
> Thanks,
>
> Subashini.K
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of RAHUL
> SURESH 
> Sent: Thursday, February 23, 2017 12:23 PM
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] deformation in simulation
>
> Simulating a protein with 100residues for 200ns doesn't show any stability.
> There are some deformation(long-bonds) in the structure throughout the
> process. Why is that so? Can I choose any stable structure in between these
> 200ns, for example say 176ns. Or is there any other way to make them work
> good.I need your valuable suggestions
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
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Re: [gmx-users] deformation in simulation

[Amir Zeb]

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 equilibrations and then production
> file.
> >
> >
> > At first, run a restrained equilibrium.
> >
> >
> > Then non-restrained equilibrium followed by production file.
> >
> >
> > Do not know the aim of your simulations.
> >
> >
> > Hope this answer helps.
> >
> >
> > Thanks,
> >
> > Subashini.K
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of RAHUL
> > SURESH 
> > Sent: Thursday, February 23, 2017 12:23 PM
> > To: gmx-us...@gromacs.org
> > Subject: [gmx-users] deformation in simulation
> >
> > Simulating a protein with 100residues for 200ns doesn't show any
> stability.
> > There are some deformation(long-bonds) in the structure throughout the
> > process. Why is that so? Can I choose any stable structure in between
> these
> > 200ns, for example say 176ns. Or is there any other way to make them work
> > good.I need your valuable suggestions
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > 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
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
> > maillist.sys.kth.se
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Re: [gmx-users] deformation in simulation

[Amir Zeb]

first you let me know, you have produced your md run or not?
xtc file is the output of md production, if you didn't actually simulate
yet, how can you get xtc file?

On Thu, Feb 23, 2017 at 12:07 AM, RAHUL SURESH <drrahulsur...@gmail.com>
wrote:

> again why XTC files are not being displayed in vmd
> ?
>
>
> On Thu, Feb 23, 2017 at 1:34 PM, Amir Zeb <zebami...@gmail.com> wrote:
>
> > so what did you find?
> > Did you fix the problem?
> >
> > On Wed, Feb 22, 2017 at 11:51 PM, Subashini .K <subashi...@hotmail.com>
> > 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.
> > >
> > >
> > > Do not know the aim of your simulations.
> > >
> > >
> > > Hope this answer helps.
> > >
> > >
> > > Thanks,
> > >
> > > Subashini.K
> > >
> > > 
> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of RAHUL
> > > SURESH <drrahulsur...@gmail.com>
> > > Sent: Thursday, February 23, 2017 12:23 PM
> > > To: gmx-us...@gromacs.org
> > > Subject: [gmx-users] deformation in simulation
> > >
> > > Simulating a protein with 100residues for 200ns doesn't show any
> > stability.
> > > There are some deformation(long-bonds) in the structure throughout the
> > > process. Why is that so? Can I choose any stable structure in between
> > these
> > > 200ns, for example say 176ns. Or is there any other way to make them
> work
> > > good.I need your valuable suggestions
> > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
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Re: [gmx-users] Extending a program

[Amir Zeb]

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 file.?
>
> I used the command
>
>
>
> *gmx convert-tpr -s md.xtc -extend 10 -o extend.tpr*
>
> *gmx mdrun -v -deffnm extend.tpr*
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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Re: [gmx-users] deformation in simulation

[Amir Zeb]

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 some deformation(long-bonds) in the structure throughout the
> process. Why is that so? Can I choose any stable structure in between these
> 200ns, for example say 176ns. Or is there any other way to make them work
> good.I need your valuable suggestions
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
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Re: [gmx-users] deformation in simulation

[Amir Zeb]

how do you visualize your system structure?

On Wed, Feb 22, 2017 at 10:58 PM, RAHUL SURESH <drrahulsur...@gmail.com>
wrote:

> Dear amir
>
> They are forming long bonds. I hope you understand what i mean. Like few
> molecules move away from the protein still bonded. and they again converge
> at some point but again they do deform.
>
>
>
> On Thu, Feb 23, 2017 at 12:26 PM, Amir Zeb <zebami...@gmail.com> 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
> >
> > All the best!
> >
> > On Wed, Feb 22, 2017 at 10:53 PM, RAHUL SURESH <drrahulsur...@gmail.com>
> > wrote:
> >
> > > Simulating a protein with 100residues for 200ns doesn't show any
> > stability.
> > > There are some deformation(long-bonds) in the structure throughout the
> > > process. Why is that so? Can I choose any stable structure in between
> > these
> > > 200ns, for example say 176ns. Or is there any other way to make them
> work
> > > good.I need your valuable suggestions
> > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
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Re: [gmx-users] deformation in simulation

[Amir Zeb]

alright
you first centralize your system by the following command
trjconv -f traj.xtc -s md.tpr -n index.ndx -o md.xtc -pbc mol -ur compact
and then visualize
probably you would have solved it. This is some how visualization  problem.

On Wed, Feb 22, 2017 at 11:06 PM, RAHUL SURESH <drrahulsur...@gmail.com>
wrote:

> using VMD
>
> On Thu, Feb 23, 2017 at 12:32 PM, Amir Zeb <zebami...@gmail.com> wrote:
>
> > how do you visualize your system structure?
> >
> > On Wed, Feb 22, 2017 at 10:58 PM, RAHUL SURESH <drrahulsur...@gmail.com>
> > wrote:
> >
> > > Dear amir
> > >
> > > They are forming long bonds. I hope you understand what i mean. Like
> few
> > > molecules move away from the protein still bonded. and they again
> > converge
> > > at some point but again they do deform.
> > >
> > >
> > >
> > > On Thu, Feb 23, 2017 at 12:26 PM, Amir Zeb <zebami...@gmail.com>
> 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
> > > >
> > > > All the best!
> > > >
> > > > On Wed, Feb 22, 2017 at 10:53 PM, RAHUL SURESH <
> > drrahulsur...@gmail.com>
> > > > wrote:
> > > >
> > > > > Simulating a protein with 100residues for 200ns doesn't show any
> > > > stability.
> > > > > There are some deformation(long-bonds) in the structure throughout
> > the
> > > > > process. Why is that so? Can I choose any stable structure in
> between
> > > > these
> > > > > 200ns, for example say 176ns. Or is there any other way to make
> them
> > > work
> > > > > good.I need your valuable suggestions
> > > > >
> > > > > --
> > > > > *Regards,*
> > > > > *Rahul Suresh*
> > > > > *Research Scholar*
> > > > > *Bharathiar University*
> > > > > *Coimbatore*
> > > > > --
> > > > > Gromacs Users mailing list
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> > or
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> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
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Re: [gmx-users] Fwd: residue not found in the database.

[Amir Zeb]

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 input file. Perhaps your atom and/or residue naming needs to be
fixed.

You'r input file should have the same atom names as depicted in the
corresponding forcefield.
You need to check the concerned atom name in the forcefield rtp file you
want to use, and put them both the similar.

Good luck

Amir

On Sun, Feb 12, 2017 at 9:18 PM, abbas khan  wrote:

> I'm trying to do a complex simulation in Gromacs but it is showing the
> following Error, how to solve this?
>
> 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 input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
> for all FF this problem is coming again and again.
>
> Gromacs simulation of Metalloproteins?
>
> Hi everyone, Hope you will be doing well. I'm new in the field of
> simulation and using Gromacs. , I appreciate your efforts the way you
> provided step by step tutorials. , I'm simulation a protein with cofactors
> Zinc and Magnesium. I searched on the internet and people suggested to use
> CHARMM force field but the thing is when I'm using CHARMM force field it is
> showing ZINC topology parameters not found in the database.  please suggest
> me any solution and also tell me can we use any other forcefield or not?
> --
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Re: [gmx-users] REGARDING TOPOLOGY FILE

[Amir Zeb]

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,
>
>
>
> Thank you for the reply. As I said earlier, there is one ligand molecule
> surrounded by many water molecules (680)
>
>
> Here, it is like this
>
>
> [ molecules ]
> ; Compoundnmols
>  ligand   1
>  WAT  680
>
>
> 680 seems to be a correct number. Because, it was computed as follows,
> using tleap of AMBER TOOLS 15:
>
>
> solvateBox LIG TIP4PBOX 10.0
>  Solute vdw bounding box:  9.963 8.173 7.953
>   Total bounding box for atom centers:  29.963 28.173 27.953
>   Solvent unit box: 18.860 18.867 18.860
>   Total vdw box size:   33.150 30.999 31.097 angstroms.
>   Volume: 31955.384 A^3
>   Total mass 12429.154 amu,  Density 0.646 g/cc
>   Added 680 residues.
>
> Still, there is an error.
>
>
> 
> 
> 
> -
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of tasneem
> kausar 
> Sent: Thursday, January 19, 2017 11:04 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE
>
> The error show that the number of atoms in topology file and gro file does
> not match
> In last line of topology file define the ligand molecule.
> here is the exapmle
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_A 1
> DRG 1
>
>
>
>
> On Thu, Jan 19, 2017 at 10:55 AM, Subashini .K 
> wrote:
>
> > Hi gromacs users,
> >
> >
> > Had taken one organic molecule (ligand) and many water molecules using
> > tleap of Amber tools 15.
> >
> >
> > Then generated .top and .gro file using acpype by the command,
> >
> > acpype -p com_solvated.top -x com_solvated.crd -b ligand
> >
> >
> > However, while using the same for gromacs, obtained the following error
> >
> >
> > number of coordinates in coordinate file (conf.gro, 2751)
> >  does not match topology (topol.top, 2071)
> >
> > How to fix this error?
> >
> > Thanks,
> > Subashini.K
>
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Re: [gmx-users] REGARDING TOPOLOGY FILE

[Amir Zeb]

can you please recognize that two extra atoms generated by acepype??

On Jan 19, 2017 4:00 PM, "Subashini .K" <subashi...@hotmail.com> wrote:

> Thank you very much for the reply.
>
>
> Actually, tried converting the ligand alone to .top and .gro file.
>
>
> The ligand contains only 29 atoms.
>
>
> 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 behalf of Amir Zeb <
> zebami...@gmail.com>
> Sent: Thursday, January 19, 2017 12:24 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE
>
> 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" <subashi...@hotmail.com> wrote:
>
> > Hi,
> >
> >
> >
> > Thank you for the reply. As I said earlier, there is one ligand molecule
> > surrounded by many water molecules (680)
> >
> >
> > Here, it is like this
> >
> >
> > [ molecules ]
> > ; Compoundnmols
> >  ligand   1
> >  WAT  680
> >
> >
> > 680 seems to be a correct number. Because, it was computed as follows,
> > using tleap of AMBER TOOLS 15:
> >
> >
> > solvateBox LIG TIP4PBOX 10.0
> >  Solute vdw bounding box:  9.963 8.173 7.953
> >   Total bounding box for atom centers:  29.963 28.173 27.953
> >   Solvent unit box: 18.860 18.867 18.860
> >   Total vdw box size:   33.150 30.999 31.097 angstroms.
> >   Volume: 31955.384 A^3
> >   Total mass 12429.154 amu,  Density 0.646 g/cc
> >   Added 680 residues.
> >
> > Still, there is an error.
> >
> >
> > 
> > 
> > 
> > -
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of tasneem
> > kausar <tasneemkausa...@gmail.com>
> > Sent: Thursday, January 19, 2017 11:04 AM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE
> >
> > The error show that the number of atoms in topology file and gro file
> does
> > not match
> > In last line of topology file define the ligand molecule.
> > here is the exapmle
> >
> > [ molecules ]
> > ; Compound#mols
> > Protein_chain_A 1
> > DRG 1
> >
> >
> >
> >
> > On Thu, Jan 19, 2017 at 10:55 AM, Subashini .K <subashi...@hotmail.com>
> > wrote:
> >
> > > Hi gromacs users,
> > >
> > >
> > > Had taken one organic molecule (ligand) and many water molecules using
> > > tleap of Amber tools 15.
> > >
> > >
> > > Then generated .top and .gro file using acpype by the command,
> > >
> > > acpype -p com_solvated.top -x com_solvated.crd -b ligand
> > >
> > >
> > > However, while using the same for gromacs, obtained the following error
> > >
> > >
> > > number of coordinates in coordinate file (conf.gro, 2751)
> > >  does not match topology (topol.top, 2071)
> > >
> > > How to fix this error?
> > >
> > > Thanks,
> > > Subashini.K
> >
> > --
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] REGARDING TOPOLOGY FILE

[Amir Zeb]

excellent

On Jan 19, 2017 5:48 PM, "Subashini .K" <subashi...@hotmail.com> wrote:


Thank you for the reply.


Have detected the actual problem and fixed it.


The atom numbering is different in mol2 file and hence in the acpype
generated file. Nothing wrong in it.


But, in the gro file, apart from two hydrogen atoms and one oxygen atom,
there was "EPW".


Hence, had to delete it (which was 415)


Now the .top and .gro match each other.


Simulations are fine.




From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
gromacs.org_gmx-users-boun...@maillist.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 .K" <subashi...@hotmail.com> wrote:

> Thank you very much for the reply.
>
>
> Actually, tried converting the ligand alone to .top and .gro file.
>
>
> The ligand contains only 29 atoms.
>
>
> 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 behalf of Amir Zeb <
> zebami...@gmail.com>
> Sent: Thursday, January 19, 2017 12:24 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE
>
> 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" <subashi...@hotmail.com> wrote:
>
> > Hi,
> >
> >
> >
> > Thank you for the reply. As I said earlier, there is one ligand molecule
> > surrounded by many water molecules (680)
> >
> >
> > Here, it is like this
> >
> >
> > [ molecules ]
> > ; Compoundnmols
> >  ligand   1
> >  WAT  680
> >
> >
> > 680 seems to be a correct number. Because, it was computed as follows,
> > using tleap of AMBER TOOLS 15:
> >
> >
> > solvateBox LIG TIP4PBOX 10.0
> >  Solute vdw bounding box:  9.963 8.173 7.953
> >   Total bounding box for atom centers:  29.963 28.173 27.953
> >   Solvent unit box: 18.860 18.867 18.860
> >   Total vdw box size:   33.150 30.999 31.097 angstroms.
> >   Volume: 31955.384 A^3
> >   Total mass 12429.154 amu,  Density 0.646 g/cc
> >   Added 680 residues.
> >
> > Still, there is an error.
> >
> >
> > 
> > 
> > 
> > -
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of tasneem
> > kausar <tasneemkausa...@gmail.com>
> > Sent: Thursday, January 19, 2017 11:04 AM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE
> >
> > The error show that the number of atoms in topology file and gro file
> does
> > not match
> > In last line of topology file define the ligand molecule.
> > here is the exapmle
> >
> > [ molecules ]
> > ; Compound#mols
> > Protein_chain_A 1
> > DRG 1
> >
> >
> >
> >
> > On Thu, Jan 19, 2017 at 10:55 AM, Subashini .K <subashi...@hotmail.com>
> > wrote:
> >
> > > Hi gromacs users,
> > >
> > >
> > > Had taken one organic molecule (ligand) and many water molecules using
> > > tleap of Amber tools 15.
> > >
> > >
> > > Then generated .top and .gro file using acpype by the command,
> > >
> > > acpype -p com_solvated.top -x com_solvated.crd -b ligand
> > >
> > >
> > > However, while using the same for gromacs, obtained the following
error
> > >
> > >
> > > number of coordinates in coordinate file (conf.gro, 2751)
> > >  does not match topology (topol.top, 2071)
> > >
> > > How to fix this error?
> > >
> > > Thanks,
> > > Subashini.K
> >
> > --
>
> --
> Gromacs Users mailing list
>

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[gmx-users] Free energy calculations

[Amir Zeb]

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.

Please let me know how may I calculate binding free energy in gromacs other
than MM/PBSA approach?

Thanks in advance!

Amir
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Re: [gmx-users] Protein and Ligand position restraint

[Amir Zeb]

Thank you Justin,
Got it

Amir

On Sun, Feb 26, 2017 at 7:52 AM, Justin Lemkul <jalem...@vt.edu> 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 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 want to listen to
>> your suggestions regarding:
>>
>> 1. Is it rational to restraint the position of the protein and/or ligand?
>> 2. If position restraint is necessary, which part of the system should I
>> restraint?
>> 3. Also, at which steps, I may restraint them, means NVT, NPT and md
>> production? Because the Justin tutorial mentioned the release of restraint
>> immediately after equilibration steps.
>>
>> I have co-factor FAD as the essential part of the protein, so I would like
>> to consider protein-FAD as single moiety. I searched from gmx-user archive
>> and Justin Tutorial, but I could not get a sound proof for this dilemma.
>>
>> Hope to listen to you soon
>>
>>
> The purpose of position restraints is to allow the solvent to relax around
> the solute(s) of interest without perturbing them due to the initial
> artificiality in the system.  In this regard, it is sensible to restrain
> the protein and whatever bound ligand(s) may be present during
> equilibration.  Restraints during production make no sense.  Flexibility
> and dynamics are the point of running an MD simulation :)
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
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Re: [gmx-users] Hbonds analysis

[Amir Zeb]

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, 2016 5:40 PM, "Khadija Amine"  wrote:

> Dear Gromacs users,
>
> I'm simulating a system of protein-protein complex.
> One of the interesting analysis I would like to perform is to compute H
> bonds between two important residues.
>
>  I want to  plot a graph of one specific residue located in the first
> protein (chain A) that make hydrogen bond interactions with another
> interface residue in the second protein (chain B). I just want to analyze
> how many times residue 1 make or lose the interactions with residue 2
> during the whole simulation (time frame : 20ns) .​
>
> If someone can help me make index for the residue 1 in the chain A and
> residue 2 in the chain B.
>
> Thank you
>
> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
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[gmx-users] xtc to dcd conversion

[Amir Zeb]

Hi
How can I convert xtc file of trajectory to dcd file for dccm analysis?

Thanks
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Re: [gmx-users] Analaysis

[Amir Zeb]

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 users, I want to obtain the percentage of helicity of a peptide
>> with respect to time after the simulation, how can I get it? I used the
>> "gmx
>> helix" and "gmx do_dssp" commands, but I could not get it. In addition, I
>>
>
> The last line in scount.xvg from gmx do_dssp gives you this.
>
> want to get the number of clusters and contact area of two particles with
>> respect to time, and I used "gmx clustsize" and "gmx mindist" commands,
>> but I
>> still cannot get these factors. can you please help me figure this out?
>> Thank
>>
>
> gmx clustsize has output options for number of clusters, cluster size,
> distribution, etc.
>
> If you want contact area, use gmx sasa with appropriate index groups.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
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Re: [gmx-users] Force filed for phosphorylated residues

[Amir Zeb]

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 issue?

Thanks in advance

On Sun, Dec 11, 2016 at 11:22 PM, Mark Abraham 
wrote:

> Hi,
>
> It might be easier to help you with all four of the things I asked you
> about.
>
> Mark
>
> On Mon, 12 Dec 2016 17:26 Seera Suryanarayana  wrote:
>
> > Dear Mark,
> >
> > I have used the charm36 force field. In c.tdb following atoms are there.
> >
> > ; CHARMM CTER
> >
> > [ COO-  ]
> > [ replace ]
> >  C C  CC12.011  0.34
> >  O OT1  OC15.9994  -0.67
> >  OXT  OT2  OC15.9994  -0.67
> >
> > [ add ]
> >
> >  28OT  C CA N
> >
> >  OC  15.4  -0.67-1
> >
> > [ impropers]
> >
> >  C CA OT2 OT1
> >
> > and in rtp file for GLN  with other atoms they mentioned only one 'O'
> > atom. They didn't give the terminal O atom information.
> >
> > Kindly tell me how to overcome this problem.
> >
> > Thanks in advance
> > Surya
> >
> >
> > Hi,
> >
> > What atoms do you have in that residue, what's in the c.tdb and .rtp for
> > GLN in force field and what did you choose for termini?
> >
> > Mark
> >
> >  I have one protein with phosphoserine and phosphothreonine. I want to
> >  do simulation, but I do not know which force field I have to use. None
> >  of the force field from gromacs has the information of phospho
> >  residues. Then I tried with charm36, but did work. Kindly suggest me
> >  what I can do.
> >
> >
> >  Well, CHARMM36 has everything you need included, so unless you explain
> >  what "didnot work" means (because it's the single most useless phrase
> >  in debugging
> >  anything), there's little anyone can do to help you.  Please describe
> >  exactly what the problem was (commands, output, errors, etc).
> >
> >  -Justin
> >
> >
> >
> >  Dear Justin,
> >
> >  I solved the problem. That is only the mismatching of residue names
> >  and I renamed the residues in my PDB file. Now the problem is with OXT
> >  atom at C-terminal end.I other words the exact error is "Atom OXT in
> >  residue GLN 68 was not found in rtp entry GLN with 17 atoms while
> >  sorting the atoms ". I understood the error. rtp file does not  have
> >  the atom OXT information. How could one solve this problem?
> >
> > Surya
> > Graduate student
> > India.
> > --
> > Gromacs Users mailing list
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> > posting!
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Re: [gmx-users] Force filed for phosphorylated residues

[Amir Zeb]

sorry, the ff is charm36 and charm26 is miss typed

On Sun, Dec 11, 2016 at 11:15 PM, Amir Zeb <zebami...@gmail.com> 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
> entry SER with 11 atoms
> while sorting atoms". can you please suggest me any possible solution for
> this issue?
>
> Thanks in advance
>
> Amir
>
> On Sun, Dec 11, 2016 at 10:26 PM, Seera Suryanarayana <paluso...@gmail.com
> > wrote:
>
>> Dear Mark,
>>
>> I have used the charm36 force field. In c.tdb following atoms are there.
>>
>> ; CHARMM CTER
>>
>> [ COO-  ]
>> [ replace ]
>>  C C  CC12.011  0.34
>>  O OT1  OC15.9994  -0.67
>>  OXT  OT2  OC15.9994  -0.67
>>
>> [ add ]
>>
>>  28OT  C CA N
>>
>>  OC  15.4  -0.67-1
>>
>> [ impropers]
>>
>>  C CA OT2 OT1
>>
>> and in rtp file for GLN  with other atoms they mentioned only one 'O'
>> atom. They didn't give the terminal O atom information.
>>
>> Kindly tell me how to overcome this problem.
>>
>> Thanks in advance
>> Surya
>>
>>
>> Hi,
>>
>> What atoms do you have in that residue, what's in the c.tdb and .rtp for
>> GLN in force field and what did you choose for termini?
>>
>> Mark
>>
>>  I have one protein with phosphoserine and phosphothreonine. I want to
>>  do simulation, but I do not know which force field I have to use. None
>>  of the force field from gromacs has the information of phospho
>>  residues. Then I tried with charm36, but did work. Kindly suggest me
>>  what I can do.
>>
>>
>>  Well, CHARMM36 has everything you need included, so unless you explain
>>  what "didnot work" means (because it's the single most useless phrase
>>  in debugging
>>  anything), there's little anyone can do to help you.  Please describe
>>  exactly what the problem was (commands, output, errors, etc).
>>
>>  -Justin
>>
>>
>>
>>  Dear Justin,
>>
>>  I solved the problem. That is only the mismatching of residue names
>>  and I renamed the residues in my PDB file. Now the problem is with OXT
>>  atom at C-terminal end.I other words the exact error is "Atom OXT in
>>  residue GLN 68 was not found in rtp entry GLN with 17 atoms while
>>  sorting the atoms ". I understood the error. rtp file does not  have
>>  the atom OXT information. How could one solve this problem?
>>
>> Surya
>> Graduate student
>> India.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
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>>
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Re: [gmx-users] Force filed for phosphorylated residues

[Amir Zeb]

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

On Sun, Dec 11, 2016 at 10:26 PM, Seera Suryanarayana 
wrote:

> Dear Mark,
>
> I have used the charm36 force field. In c.tdb following atoms are there.
>
> ; CHARMM CTER
>
> [ COO-  ]
> [ replace ]
>  C C  CC12.011  0.34
>  O OT1  OC15.9994  -0.67
>  OXT  OT2  OC15.9994  -0.67
>
> [ add ]
>
>  28OT  C CA N
>
>  OC  15.4  -0.67-1
>
> [ impropers]
>
>  C CA OT2 OT1
>
> and in rtp file for GLN  with other atoms they mentioned only one 'O'
> atom. They didn't give the terminal O atom information.
>
> Kindly tell me how to overcome this problem.
>
> Thanks in advance
> Surya
>
>
> Hi,
>
> What atoms do you have in that residue, what's in the c.tdb and .rtp for
> GLN in force field and what did you choose for termini?
>
> Mark
>
>  I have one protein with phosphoserine and phosphothreonine. I want to
>  do simulation, but I do not know which force field I have to use. None
>  of the force field from gromacs has the information of phospho
>  residues. Then I tried with charm36, but did work. Kindly suggest me
>  what I can do.
>
>
>  Well, CHARMM36 has everything you need included, so unless you explain
>  what "didnot work" means (because it's the single most useless phrase
>  in debugging
>  anything), there's little anyone can do to help you.  Please describe
>  exactly what the problem was (commands, output, errors, etc).
>
>  -Justin
>
>
>
>  Dear Justin,
>
>  I solved the problem. That is only the mismatching of residue names
>  and I renamed the residues in my PDB file. Now the problem is with OXT
>  atom at C-terminal end.I other words the exact error is "Atom OXT in
>  residue GLN 68 was not found in rtp entry GLN with 17 atoms while
>  sorting the atoms ". I understood the error. rtp file does not  have
>  the atom OXT information. How could one solve this problem?
>
> Surya
> Graduate student
> India.
> --
> Gromacs Users mailing list
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Re: [gmx-users] Force filed for phosphorylated residues

[Amir Zeb]

thanks to all of you for your advice

amrir

On Mon, Dec 12, 2016 at 4:04 AM, Justin Lemkul <jalem...@vt.edu> 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 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?
>>
>>
> "SER" is normal serine.  "SP1" is monoanionic phosphoserine, "SP2" is
> dianionic.  The residue name and the atom names have to match the
> expectations of the .rtp file.  Read it to determine if everything checks
> out.
>
> -Justin
>
>
> Thanks in advance
>>
>> Amir
>>
>> On Sun, Dec 11, 2016 at 10:26 PM, Seera Suryanarayana <
>> paluso...@gmail.com>
>> wrote:
>>
>> Dear Mark,
>>>
>>> I have used the charm36 force field. In c.tdb following atoms are there.
>>>
>>> ; CHARMM CTER
>>>
>>> [ COO-  ]
>>> [ replace ]
>>>  C C  CC12.011  0.34
>>>  O OT1  OC15.9994  -0.67
>>>  OXT  OT2  OC15.9994  -0.67
>>>
>>> [ add ]
>>>
>>>  28OT  C CA N
>>>
>>>  OC  15.4  -0.67-1
>>>
>>> [ impropers]
>>>
>>>  C CA OT2 OT1
>>>
>>> and in rtp file for GLN  with other atoms they mentioned only one 'O'
>>> atom. They didn't give the terminal O atom information.
>>>
>>> Kindly tell me how to overcome this problem.
>>>
>>> Thanks in advance
>>> Surya
>>>
>>>
>>> Hi,
>>>
>>> What atoms do you have in that residue, what's in the c.tdb and .rtp for
>>> GLN in force field and what did you choose for termini?
>>>
>>> Mark
>>>
>>>  I have one protein with phosphoserine and phosphothreonine. I want to
>>>  do simulation, but I do not know which force field I have to use. None
>>>  of the force field from gromacs has the information of phospho
>>>  residues. Then I tried with charm36, but did work. Kindly suggest me
>>>  what I can do.
>>>
>>>
>>>  Well, CHARMM36 has everything you need included, so unless you explain
>>>  what "didnot work" means (because it's the single most useless phrase
>>>  in debugging
>>>  anything), there's little anyone can do to help you.  Please describe
>>>  exactly what the problem was (commands, output, errors, etc).
>>>
>>>  -Justin
>>>
>>>
>>>
>>>  Dear Justin,
>>>
>>>  I solved the problem. That is only the mismatching of residue names
>>>  and I renamed the residues in my PDB file. Now the problem is with OXT
>>>  atom at C-terminal end.I other words the exact error is "Atom OXT in
>>>  residue GLN 68 was not found in rtp entry GLN with 17 atoms while
>>>  sorting the atoms ". I understood the error. rtp file does not  have
>>>  the atom OXT information. How could one solve this problem?
>>>
>>> Surya
>>> Graduate student
>>> India.
>>> --
>>> 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
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
> --
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Re: [gmx-users] How can I calculate Potential Energy of the segment divided by index file?

[Amir Zeb]

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 Gromacs users
>
>
> I want to calculate Potential Energy of segment of the structure.
> For example, segment that coordinations in z axis are 7.2 Å in the
> structure.
>
> I could specify that segment of atom numbers by writing index file.
> But gmx energy has no option of specifying segments by index file.
>
> Then, how should I get the Potential Energy of segments?
> Could you tell me how to solve this problem, please?
>
> Sincerely.
>
>
> Keisuke Ohki.
> --
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Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

alright
why do you care of forcefield in terms of free energy calculations?
do you have literature in reference for your protein simulated with a
specific ff?

On Jan 7, 2017 1:38 PM, "tasneem kausar" <tasneemkausa...@gmail.com> wrote:

> mm/pbsa calculates binding energy. I have used that.
>
> On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb <zebami...@gmail.com> 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" <tasneemkausa...@gmail.com>
> > 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 mehtane in
> water.
> > > That calculation are performed on a neutral system. If the ligand
> > molecule
> > > has charge what are the provisions that could be taken into account.
> > > I have performed my MD simulation using force field gromos54a7. And
> Now I
> > > am trying to go onward using free energy calculations. Since the free
> > > energy calculations are performed on ambed99ldn, opls and charmm force
> > > fields (as I know from the articles). Is it okay to use gromos54a7 ff
> for
> > > free energy calculations.
> > >
> > > Kindly tell me
> > >
> > > Thanks in Advance
> > > --
> > > Gromacs Users mailing list
> > >
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Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

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 mehtane in water.
> That calculation are performed on a neutral system. If the ligand molecule
> has charge what are the provisions that could be taken into account.
> I have performed my MD simulation using force field gromos54a7. And Now I
> am trying to go onward using free energy calculations. Since the free
> energy calculations are performed on ambed99ldn, opls and charmm force
> fields (as I know from the articles). Is it okay to use gromos54a7 ff for
> free energy calculations.
>
> Kindly tell me
>
> Thanks in Advance
> --
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Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

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:

> Dear all
>
> It is first time I am calculating free energy of protein and ligand. I am
> following the Justin's tutorial of methane in water free energy
> calculations. Though only van der waal lambda are defined so I have taken
> the mdp files from the alchemistry.org web page. Since the ligand and
> protein under my study have positive charges (one positive charge on ligand
> and tree positive charges on protein). So I have to add a CL ions in
> topology file to make a neutral sytem.
> Is it okay to use the system with ion for free energy calculation?
> If yes, What are change that can be made in mdp entry.
>
> Waiting for suggestions
> Thanks in Advance
> --
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Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

well
if you are confident of your simulation you may definitly go ahead with
this ff
otherwise you will have to change the ff for simulation too
i think this is not rational to simulate the system with one ff and then
change the ff for free energy calculations

good luck

On Jan 7, 2017 2:01 PM, "tasneem kausar" <tasneemkausa...@gmail.com> 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 and drug and
> topology files were generated from ATB in gromos54a7 format. Since I didn't
> find free energy calculation of protein and ligand with this force field.
> Thats why I was confused to proceed further using the same.
>
> On Sat, Jan 7, 2017 at 10:07 AM, tasneem kausar <tasneemkausa...@gmail.com
> >
> wrote:
>
> > mm/pbsa calculates binding energy. I have used that.
> >
> > On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb <zebami...@gmail.com> 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" <tasneemkausa...@gmail.com>
> >> 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 mehtane in
> water.
> >> > That calculation are performed on a neutral system. If the ligand
> >> molecule
> >> > has charge what are the provisions that could be taken into account.
> >> > I have performed my MD simulation using force field gromos54a7. And
> Now
> >> I
> >> > am trying to go onward using free energy calculations. Since the free
> >> > energy calculations are performed on ambed99ldn, opls and charmm force
> >> > fields (as I know from the articles). Is it okay to use gromos54a7 ff
> >> for
> >> > free energy calculations.
> >> >
> >> > Kindly tell me
> >> >
> >> > Thanks in Advance
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at http://www.gromacs.org/
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> >> > send a mail to gmx-users-requ...@gromacs.org.
> >> >
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Re: [gmx-users] Fix the residues

[Amir Zeb]

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 users,
>
> I am trying to run a md using 4n6p.cif, which was obtained from PDB. I
> converted the file into pdb format using DS4.1, and got the file named
> lactoferrin.pdb. When I directly run
> the command "gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water
> spce", the program runs and produces the information as follows:
> ...
> WARNING: WARNING: Residue 1 named TYR of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom H used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
> WARNING: WARNING: Residue 335 named SER of a molecule in the input file
> was mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
> ...
> How should I fix the residues? And which tools should I use? Is there any
> examples or tutorials?
>
> If anyone can suggest a solution to this issue, it would be really helpful.
>
>
>
>
>
>
>
> --
>
> With my best wishes,
> Ming Li, PhD
> Chinese Academy of Agricultural Sciences, Beijing, China
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Re: [gmx-users] how to compute charged carried by a single residue

[Amir Zeb]

Thanks Mark for your quick response,

I did as you mentioned, what i got was actually the total charge of the
each residue remained constant at the end.
What i'm interested in, is that i have to analyze my results and it seems
that there is loss of electrostatic interaction for a mutated residue but i
don't know how to calculate this loss.
Please let me know if you have kindly meet my question?/

Thanks Mark.

Amir

On Tue, Dec 20, 2016 at 2:14 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> You open your topology file in a text editor and see what it is :-)
>
> Mark
>
> On Tue, Dec 20, 2016 at 9:12 PM Amir Zeb <zebami...@gmail.com> 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
> >
> > Thanks
> > --
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[gmx-users] Clustsize error

[Amir Zeb]

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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[gmx-users] Homology model refinement

[Amir Zeb]

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 inhibitor bound in template structure. But before to reach that
stage, i want to simulate the created model to refine the structure which
is a common practice in modelling. I'm not pretty sure that should i
simulate the model structure along with the inhibitor and co-factor from
template, or one of them, or just only the protein structure alone? Please
let me, if you have any referenced answer.

Regards

Amir
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Re: [gmx-users] Homology model refinement

[Amir Zeb]

Hi Mark,

I want to refine the model for any bad contact if the structure has. This
article support the simulation of any homology model after its creation by
homology modeling approach "
https://www.ncbi.nlm.nih.gov/pubmed/22513870?dopt=Abstract;. Do you please
think that there is no need to refine the model via simulation? or the
claim which i do for refinement via simulation, is biased?

Thanks for consideration!

Amir

On Wed, Dec 21, 2016 at 10:09 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> What us the purpose in doing MD on the homology model? That'll tell you
> whether you need a model with the other parts.
>
> Mark
>
> On Thu, 22 Dec 2016 16:51 Amir Zeb <zebami...@gmail.com> 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 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 inhibitor bound in template structure. But before to reach that
> > stage, i want to simulate the created model to refine the structure which
> > is a common practice in modelling. I'm not pretty sure that should i
> > simulate the model structure along with the inhibitor and co-factor from
> > template, or one of them, or just only the protein structure alone?
> Please
> > let me, if you have any referenced answer.
> >
> > Regards
> >
> > Amir
> > --
> > Gromacs Users mailing list
> >
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> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Protein-Ligand Complex MD simulation: Restrain protein alone or Restrain both protein and ligand during simulation?

[Amir Zeb]

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
> simulation using Gromacs 5.1.4 to check.
>
>  1. What sought of MD simulation we have to perform?.
>  2. Restrain protein alone or Restrain both protein and ligand during
> simulation?.
>  3. What is the exact command for Drug positional RMSD plot?
>  4. What is the exact command for Number of Hydrogen bond plot?
>  5. What is the exact command for Other interactions between protein and
> ligand?
>  6. how to view the trajectory files? or We have to convert the frames to
> *.pdb and view in Pymol?
>
> Regards,
> Adarsh V. K.
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Re: [gmx-users] Homology model refinement

[Amir Zeb]

Hi Mark,

Thanks for your response. I did for simulation for both the systems 1. only
protein 2. protein with co-factor. By the way, I'm not pretty sure, but I'm
relying on rmsd of C-alpha to evaluate the structure's stability. In both
the cases, the rmsd range was highly wide ~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 <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> On Thu, Dec 22, 2016 at 5:19 PM Amir Zeb <zebami...@gmail.com> wrote:
>
> > Hi Mark,
> >
> > I want to refine the model for any bad contact if the structure has.
>
>
> So, do you expect the structure to be stable in the absence of the other
> things? That tells you whether you need to attempt refinement with the
> other things, or not.
>
> Mark
>
>
> > This
> > article support the simulation of any homology model after its creation
> by
> > homology modeling approach "
> > https://www.ncbi.nlm.nih.gov/pubmed/22513870?dopt=Abstract;. Do you
> please
> > think that there is no need to refine the model via simulation? or the
> > claim which i do for refinement via simulation, is biased?
> >
> > Thanks for consideration!
> >
> > Amir
> >
> > On Wed, Dec 21, 2016 at 10:09 PM, Mark Abraham <mark.j.abra...@gmail.com
> >
> > wrote:
> >
> > > Hi,
> > >
> > > What us the purpose in doing MD on the homology model? That'll tell you
> > > whether you need a model with the other parts.
> > >
> > > Mark
> > >
> > > On Thu, 22 Dec 2016 16:51 Amir Zeb <zebami...@gmail.com> 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 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 inhibitor bound in template structure. But before to reach
> > that
> > > > stage, i want to simulate the created model to refine the structure
> > which
> > > > is a common practice in modelling. I'm not pretty sure that should i
> > > > simulate the model structure along with the inhibitor and co-factor
> > from
> > > > template, or one of them, or just only the protein structure alone?
> > > Please
> > > > let me, if you have any referenced answer.
> > > >
> > > > Regards
> > > >
> > > > Amir
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
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> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
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Re: [gmx-users] Homology model refinement

[Amir Zeb]

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,
>
> What is your target structure size? If you want to perform explicit solvent
> simulation for bigger protein, it may be time-consuming simulation.
> My suggestion is that you can run simulation implicitly, it helps you
> remove some bad contacts. Then, you can make cluster analysis and find
> dominating configurations from section that converged to stable rmsd
> values.
>
> Mijiddorj
>
> > > 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 inhibitor bound in template structure. But before to reach
> > that
> > > > stage, i want to simulate the created model to refine the structure
> > which
> > > > is a common practice in modelling. I'm not pretty sure that should i
> > > > simulate the model structure along with the inhibitor and co-factor
> > from
> > > > template, or one of them, or just only the protein structure alone?
> > > Please
> > > > let me, if you have any referenced answer.
> > > >
> > > > Regards
> > > >
> > > > Amir
> > > > --
> >
> >
> --
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[gmx-users] how to compute charged carried by a single residue

[Amir Zeb]

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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Re: [gmx-users] how to compute charged carried by a single residue

[Amir Zeb]

alright Mark,

Thanks a lot


On Tue, Dec 20, 2016 at 3:00 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> On Tue, Dec 20, 2016 at 9:20 PM Amir Zeb <zebami...@gmail.com> wrote:
>
> > Thanks Mark for your quick response,
> >
> > I did as you mentioned, what i got was actually the total charge of the
> > each residue remained constant at the end.
> >
>
> Your topology isn't changing over the simulation, so you shouldn't expect
> it to change.
>
> What i'm interested in, is that i have to analyze my results and it seems
> > that there is loss of electrostatic interaction for a mutated residue
> but i
> > don't know how to calculate this loss.
> > Please let me know if you have kindly meet my question?/
> >
>
> Your force field does not permit such a decomposition to be meaningful.
> There are ways to compute a change in free-energy of binding upon such a
> mutation
>
> Mark
>
> Thanks Mark.
> >
> > Amir
> >
> > On Tue, Dec 20, 2016 at 2:14 AM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > You open your topology file in a text editor and see what it is :-)
> > >
> > > Mark
> > >
> > > On Tue, Dec 20, 2016 at 9:12 PM Amir Zeb <zebami...@gmail.com> 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
> > > >
> > > > Thanks
> > > > --
> > > > Gromacs Users mailing list
> > > >
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> > > > posting!
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[gmx-users] FAD parameters in CHRAMm36 ff

[Amir Zeb]

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
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Re: [gmx-users] FAD parameters in CHRAMm36 ff

[Amir Zeb]

Thanks Dr. Justin for your reply

On Fri, Mar 31, 2017 at 6:11 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 3/31/17 3:54 AM, Vytautas Rakeviius wrote:
>
>> I think you should use cgenff for FAD in such case. They are compatible
>> and can by used together.
>>
>>
> Indeed, though one should pay close attention to the parameter penalties
> in the adenine nucleotide portion of the molecule, as that part is covered
> by standard CHARMM.  Any deviations should be investigated, though they
> will probably be small and therefore unimportant.  Most of the necessary
> 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 <zebami...@gmail.com>
>> wrote:
>>
>>
>>  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
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Error in free energy calculation

[Amir Zeb]

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:

> Dear All
>
> I am trying to perform free energy calculations of a protein drug system.
> I am using Gromacs-5.1.4 for this purpose. decoulpe molecule type i.e. drug
> molecule is defined in separate drug.itp file. From the discussions of
> mailing list I have found that this is not a problem. To obtain the
> equilibrium values for protein-ligand restraint 15 ns simulation was
> performed. Here is the last section of topology file.
>  ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> #include "drug.itp"
> [ intermolecular_interactions ]
> [ bonds ]
> ;i j  type r0A r1A r2AfcAr0B r1B r2B
> fcB
>   1444  311810 0.591   0.591   10.0   0.00.591   0.591   10.0
> 4184.000
>
> [ angle_restraints ]
> ;   aiajakal  typethA  fcAmultA  thB  fcB
> multB
>   1431  1444  3118  1444 152.350.0152.3541.8401
>   1444  3118  3120  3118 1   118.140.01   118.1441.8401
>
> [ dihedral_restraints ]
> ;   aiajakal  typephiA dphiA  fcAphiB  dphiB
> fcB
>   1444  1431  1444  3118 1-99.41   0.00.0-99.410.0
> 41.840
>   1431  1444  3118  3120 1 17.490.00.017.490.0
> 41.840
>   1444  3118  3120  3119 1 -6.49   0.00.0 -6.490.0
> 41.840
> ; Include water topology
> #include "gromos54a7.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
> #endif
>
> ; Include topology for ions
> #include "gromos54a7.ff/ions.itp"
>
> [ system ]
> ; Name
> DUMM in water t= 1.0
> [ molecules ]
> ; Compound#mols
> Protein_chain_A 1
> DRG 1
> SOL 17685
>
> Is there any default position for [ intermolecular_interaction ] in
> topology file.
> Since I am using a drug.itp file for drug molecule. Numbering in itp file
> starts from 1. Is atom number in itp file needed to be modified?
>
>
> grompp gives many warning  and 1 error
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9#
>
> WARNING 1 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_geometry' in parameter file
>
>
>
> WARNING 2 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_dim' in parameter file
>
>
>
> WARNING 3 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_start' in parameter file
>
>
>
> WARNING 4 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_init1' in parameter file
>
>
>
> WARNING 5 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_ngroups' in parameter file
>
>
>
> WARNING 6 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_group0' in parameter file
>
>
>
> WARNING 7 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_group1' in parameter file
>
>
>
> WARNING 8 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_k1' in parameter file
>
>
>
> WARNING 9 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_kB1' in parameter file
>
>
>
> NOTE 1 [file em_steep_0.mdp]:
>   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>   that with the Verlet scheme, nstlist has no effect on the accuracy of
>   your simulation.
>
> Setting the LD random seed to 1259182625
> Generated 226 of the 1711 non-bonded parameter combinations
>
> ---
> Program gmx grompp, VERSION 5.1.4
> Source code file:
> /home/shahid/Software/gromacs-5.1.4/src/gromacs/gmxpreprocess/topio.c,
> line: 755
>
> Fatal error:
> Syntax error - File complex.top, line 19956
> Last line read:
> '[ intermolecular_interactions ]'
> Invalid order for directive intermolecular_interactions
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Here are mdp parameters
>
> ; Options for the decoupling
> sc-alpha = 0.5
> sc-coul  = no
> sc-power = 1
> sc-sigma = 0.3
> couple-moltype   = DRG
> couple-lambda0   = none
> couple-lambda1   = vdw-q
> couple-intramol  = no
> nstdhdl  = 10
> ; No velocities during EM
> gen_vel  = no
> ; options for bonds
> constraints  = all_bonds
> constraint-algorithm = lincs
> continuation = no
> lincs-order  = 12
> pull   = no
> pull_geometry  = distance
> pull_dim   = N N Y
> 

Re: [gmx-users] How to access recent discussion on gmx-user list?

[Amir Zeb]

Thanks a lot Das,

You really solved my problem.

Amir

On Mon, Mar 20, 2017 at 3:06 AM, Devashish_Das <dasdevashish...@gmail.com>
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 <zebami...@gmail.com> wrote:
>
> > 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 the link to access the updated discussion.
> >
> > Thanks
> >
> > Amir
> > --
> > 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 (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
>
> Regards,
>
> Devashish Das
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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[gmx-users] How to access recent discussion on gmx-user list?

[Amir Zeb]

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 the link to access the updated discussion.

Thanks

Amir
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Re: [gmx-users] powercut command

[Amir Zeb]

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 stops..
> To continue my MD, I use command:-
>
>
> gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi 10ns.cpt
> -cpo 10ns.cpt -append
>
>
>
> but shows error.
>
>
> Error in user input:
> Invalid command-line options
> Unknown command-line option -md_1_0.xtc
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> [root@dhcppc58 AhpE_MSH]#
>
>
>
> Plzz.. help me out
> --
> 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
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[gmx-users] Regarding Umbrella sampling

[Amir Zeb]

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 pull.mdp, line 65]:
  Unknown left-hand 'pull_group1_name' in parameter file



WARNING 4 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_group2_name' in parameter file



WARNING 5 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_coord1_type' in parameter file



WARNING 6 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_coord1_geometry' in parameter file



WARNING 7 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_coord1_groups' in parameter file



WARNING 8 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_coord1_dim' in parameter file



WARNING 9 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_coord1_rate' in parameter file



WARNING 10 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_coord1_k' in parameter file



WARNING 11 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_coord1_start' in parameter file



There was 1 note

There were 11 warnings


*The pull.mdp file is this one:*

title   = Umbrella pulling simulation
define  = -DPOSRES_NAD
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 25; 500 ps
nstcomm = 10
; Output parameters
nstxout = 5000  ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout   = 500   ; every 1 ps
nstenergy   = 500
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes   ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = Protein   NAD
tau_t   = 0.5   0.5
ref_t   = 310   310
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= NAD
pull_group2_name= Protein
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0


Please let me know where I'm making the mistake.

Regards!

-Amir
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Re: [gmx-users] Regarding Umbrella sampling

[Amir Zeb]

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 <jalem...@vt.edu> wrote:

>
>
> On 3/8/17 8:11 PM, Amir Zeb wrote:
>
>> 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 pull.mdp, line 65]:
>>   Unknown left-hand 'pull_group1_name' in parameter file
>>
>>
>>
>> WARNING 4 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_group2_name' in parameter file
>>
>>
>>
>> WARNING 5 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_coord1_type' in parameter file
>>
>>
>>
>> WARNING 6 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_coord1_geometry' in parameter file
>>
>>
>>
>> WARNING 7 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_coord1_groups' in parameter file
>>
>>
>>
>> WARNING 8 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_coord1_dim' in parameter file
>>
>>
>>
>> WARNING 9 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_coord1_rate' in parameter file
>>
>>
>>
>> WARNING 10 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_coord1_k' in parameter file
>>
>>
>>
>> WARNING 11 [file pull.mdp, line 65]:
>>   Unknown left-hand 'pull_coord1_start' in parameter file
>>
>>
>>
>> There was 1 note
>>
>> There were 11 warnings
>>
>>
>> *The pull.mdp file is this one:*
>>
>>
>> title   = Umbrella pulling simulation
>> define  = -DPOSRES_NAD
>> ; Run parameters
>> integrator  = md
>> dt  = 0.002
>> tinit   = 0
>> nsteps  = 25; 500 ps
>> nstcomm = 10
>> ; Output parameters
>> nstxout = 5000  ; every 10 ps
>> nstvout = 5000
>> nstfout = 500
>> nstxtcout   = 500   ; every 1 ps
>> nstenergy   = 500
>> ; Bond parameters
>> constraint_algorithm= lincs
>> constraints = all-bonds
>> continuation= yes   ; continuing from NPT
>> ; Single-range cutoff scheme
>> nstlist = 5
>> ns_type = grid
>> rlist   = 1.4
>> rcoulomb= 1.4
>> rvdw= 1.4
>> ; PME electrostatics parameters
>> coulombtype = PME
>> fourierspacing  = 0.12
>> fourier_nx  = 0
>> fourier_ny  = 0
>> fourier_nz  = 0
>> pme_order   = 4
>> ewald_rtol  = 1e-5
>> optimize_fft= yes
>> ; Berendsen temperature coupling is on in two groups
>> Tcoupl  = Nose-Hoover
>> tc_grps = Protein   NAD
>> tau_t   = 0.5   0.5
>> ref_t   = 310   310
>> ; Pressure coupling is on
>> Pcoupl  = Parrinello-Rahman
>> pcoupltype  = isotropic
>> tau_p   = 1.0
>> compressibility = 4.5e-5
>> ref_p   = 1.0
>> refcoord_scaling = com
>> ; Generate velocities is off
>> gen_vel = no
>> ; Periodic boundary conditions are on in all directions
>> pbc = xyz
>> ; Long-range dispersion correction
>> DispCorr= EnerPres
>> ; Pull code
>> pull= yes
>> pull_ngroups= 2
>> pull_ncoords= 1
>> pull_group1_name= NAD
>> pull_group2_name= Protein
>> pull_coord1_type= umbrella  ; harmonic biasing force
>> pull_coord1_geometry= distance  ; simple distance increase
>> pull_coord1_groups  = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per ns
>> pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
>> pull_coord1_start   = yes   ; define initial COM distance > 0
>>
>>
>> Please let me know where I'm making the mistake.
>>
>>
> You're using an outdated version of GROMACS that does not recognize the
> new syntax that was introduced in version 5.1.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Ph

Re: [gmx-users] Regarding Umbrella sampling

[Amir Zeb]

Thanks Justin,

Got it

-Amir

On Wed, Mar 8, 2017 at 7:08 PM, Justin Lemkul <jalem...@vt.edu> 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 version. Can you please let me know how to get files
>> compatible
>> for this version?
>>
>>
> You'll either have to translate the appropriate options to the old syntax:
>
> http://manual.gromacs.org/archive/5.0.6/online/mdp_opt.html#pull
>
> or upgrade to a current version of GROMACS (a much better and more
> productive idea).
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> 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
>
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Re: [gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing

[Amir Zeb]

Thanks Dr. Justin,

Got it

-Amir

On Fri, Mar 3, 2017 at 5:00 AM, Justin Lemkul <jalem...@vt.edu> 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 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?
>>
>>
> I have said nothing about the suitability of the force field; it's
> perfectly fine to use (though I think more modern versions, e.g. C36 and
> C36m are generally preferable).
>
> I'm really just being pedantic and trying to prevent more errors from
> entering the literature.  There is no such thing as a "CHARMM27 protein
> force field."  It gets lumped into "CHARMM27" based solely on file naming.
> The parameters in GROMACS that are labeled "charmm27.ff" are actually
> CHARMM22/CMAP with various revisions that have appeared in the literature
> over several years before CHARMM36 was released.  So anyone claiming to use
> "CHARMM27" as their protein force field is using a misnomer.  For the sake
> of accuracy, I am trying to encourage people to break this habit and use
> the proper name of the force field.
>
> Just because it's published, doesn't mean it's right :)
>
> -Justin
>
>
> Thanks
>>
>> -Amir
>>
>> On Thu, Mar 2, 2017 at 2:10 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>>
>>> On 3/2/17 2:16 PM, Sanim Rahman wrote:
>>>
>>> Hi all,
>>>>
>>>> I am attempting to run a membrane protein simulation where I am
>>>> describing
>>>> my protein and solvent in terms of CHARMM27 and my lipids in CHARMM36.
>>>> When
>>>> I use the grompp command, I get the following error:
>>>>
>>>> Fatal error:
>>>> Syntax error - File forcefield.itp, line 9
>>>> Last line read:
>>>> '[ defaults ]'
>>>> Invalid order for directive defaults
>>>>
>>>> To create my topology file, I took my protein.top and at the bottom
>>>> included my lipid.itp and solvent.itp. The error is referencing to my
>>>> charmm36 force field file. I was unsure what to do so I just removed the
>>>> line with [ defaults ] on it and tried running it again. This time I
>>>> received this error:
>>>>
>>>> Fatal error:
>>>> Syntax error - File ffnonbonded.itp, line 5
>>>> Last line read:
>>>> '[ atomtypes ]'
>>>> Invalid order for directive atomtypes
>>>>
>>>> Is the source of the error from how my topology files are processing the
>>>> force field files since I am using both CHARMM27 and CHARMM36? I read a
>>>> previous thread that you can't have two [ default ] lines which make
>>>> sense
>>>> but I am unsure of what is the proper protocol to get around this to
>>>> include both force fields. Any help will be deeply appreciated!
>>>>
>>>>
>>>> I mentioned this last week in another thread, but I'll say it again:
>>> "CHARMM27" is not a valid identifier for a protein force field.  What
>>> you're trying to use is CHARMM22/CMAP.
>>>
>>> The bigger question is why you want to use this combination?  It may not
>>> be practical or possible to do so in GROMACS.  You'll likely have to hack
>>> out the bonded and nonbonded parameters that relate to proteins and marry
>>> them together with the lipid-only portions of CHARMM36.
>>>
>>> -Justin
>>>
>>> Thank You,
>>>
>>>>
>>>> *Sanim Rahman*
>>>> B.S. Chemical Engineering, 2019
>>>> Resident Assistant, Castor Hall Engineering Living Learning Community
>>>> 2016-2017
>>>> Co-Founder and Co-President of the Undergraduate Research Society
>>>> Undergraduate Researcher, Global Center for Hearing and Speech Research
>>>>
>>>>
>>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Ba

Re: [gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing

[Amir Zeb]

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?

Thanks

-Amir

On Thu, Mar 2, 2017 at 2:10 PM, Justin Lemkul  wrote:

>
>
> On 3/2/17 2:16 PM, Sanim Rahman wrote:
>
>> Hi all,
>>
>> I am attempting to run a membrane protein simulation where I am describing
>> my protein and solvent in terms of CHARMM27 and my lipids in CHARMM36.
>> When
>> I use the grompp command, I get the following error:
>>
>> Fatal error:
>> Syntax error - File forcefield.itp, line 9
>> Last line read:
>> '[ defaults ]'
>> Invalid order for directive defaults
>>
>> To create my topology file, I took my protein.top and at the bottom
>> included my lipid.itp and solvent.itp. The error is referencing to my
>> charmm36 force field file. I was unsure what to do so I just removed the
>> line with [ defaults ] on it and tried running it again. This time I
>> received this error:
>>
>> Fatal error:
>> Syntax error - File ffnonbonded.itp, line 5
>> Last line read:
>> '[ atomtypes ]'
>> Invalid order for directive atomtypes
>>
>> Is the source of the error from how my topology files are processing the
>> force field files since I am using both CHARMM27 and CHARMM36? I read a
>> previous thread that you can't have two [ default ] lines which make sense
>> but I am unsure of what is the proper protocol to get around this to
>> include both force fields. Any help will be deeply appreciated!
>>
>>
> I mentioned this last week in another thread, but I'll say it again:
> "CHARMM27" is not a valid identifier for a protein force field.  What
> you're trying to use is CHARMM22/CMAP.
>
> The bigger question is why you want to use this combination?  It may not
> be practical or possible to do so in GROMACS.  You'll likely have to hack
> out the bonded and nonbonded parameters that relate to proteins and marry
> them together with the lipid-only portions of CHARMM36.
>
> -Justin
>
> Thank You,
>>
>> *Sanim Rahman*
>> B.S. Chemical Engineering, 2019
>> Resident Assistant, Castor Hall Engineering Living Learning Community
>> 2016-2017
>> Co-Founder and Co-President of the Undergraduate Research Society
>> Undergraduate Researcher, Global Center for Hearing and Speech Research
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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[gmx-users] membrane-protein simulation

[Amir Zeb]

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_POSRES.
Once I tried the minimization of the system before the shrinking step, I
got the error as below:

Fatal error:
[ file strong_posre.itp, line 548 ]:
Atom index (544) in position_restraints out of bounds (1-543).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I tried so many options but could not fix the issue. Please keep in view
that the same procedure is working well with a single chain of the protein.
Kindly help me how to fix this issue?

Thanks in advance
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Re: [gmx-users] membrane-protein simulation

[Amir Zeb]

Thanks Justin

Got it, it's working.

On Wed, Aug 2, 2017 at 10:02 AM, Justin Lemkul <jalem...@vt.edu> 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 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_POSRES.
>> Once I tried the minimization of the system before the shrinking step, I
>> got the error as below:
>>
>> Fatal error:
>> [ file strong_posre.itp, line 548 ]:
>> Atom index (544) in position_restraints out of bounds (1-543).
>> This probably means that you have inserted topology section
>> "position_restraints"
>> in a part belonging to a different molecule than you intended to.
>> In that case move the "position_restraints" section to the right molecule.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> I tried so many options but could not fix the issue. Please keep in view
>> that the same procedure is working well with a single chain of the
>> protein.
>> Kindly help me how to fix this issue?
>>
>>
> You need to create restraint files for each chain separately and include
> them in each [moleculetype] separately, as explained here:
>
> http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_
> position_restraints_out_of_bounds
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] MM/PBSA

[Amir Zeb]

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 .itp files.  But when run the command,
am getting an error saying "NO XTC" Could someone help me, what would be
wrong, why such error occurs. i have pasted the error message below.


Thank you!


Select a group:
---
Program trjconv_mpi, VERSION 4.5.5
Source code file: trxio.c, line: 832

Fatal error:
No XTC!

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"You Could Make More Money As a Butcher" (F. Zappa)

Select group for least squares fit
Selected 27: 'complex'
Select group for centering
Selected 27: 'complex'
Select group for output
Selected 27: 'complex'
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[gmx-users] trans-membrane protein simulation

[Amir Zeb]

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 condition) during the
simulation.

Will it please be recommended to follow the* Justin tutorial *for membrane
protein simulation (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html)
or I should make some modifications to this tutorial? Also, please suggest
me whether this kind of simulation in heterogeneous condition is worth
enough to get reliable data or not?

Thanks
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[gmx-users] Distances calculation in umbrella sampling

[Amir Zeb]

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 given by Dr.
Justin in his tutorial. I have replaced the Chain_A by ligand name and
Chain_B by Protein_ZN in original script to represent my index file groups.
The summary_distances.dat file is generating successfully, but it has no
distances information. Only frames number are given on a single column and
is repeated again after 500th frame. The summary_distances.dat file is
attached for your kind consideration.
Please let me know if there is any possibility to fix this issue.

Thanks in advance!
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Re: [gmx-users] Distances calculation in umbrella sampling

[Amir Zeb]

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.
>>
>
> Or run one instance of gmx distance manually to understand how to properly
> use it, diagnose any problems in your selection, etc. and fix the script.
> There's no reason to reinvent the wheel, just modify the script properly to
> suit your needs.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
>
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Re: [gmx-users] Problem with topology generation by Amber 12 ff

[Amir Zeb]

Thanks Dr. Justin,

The atoms of Histidine residue formed the dihedral CB, CG, ND1 and CD2.
Tracing the residues rtp file in Amber12 ff, I should assign His either HID
or HIE, But once I protonate HIS at NE2 only and assign this NE2-protonated
HIS as HIE, some of the residues other than this 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 <jalem...@vt.edu> wrote:

>
>
> On 12/4/17 1:45 AM, Amir Zeb wrote:
>
>> 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 such error. I
>> searched out the solution on google but could not find the answer.
>>
>> Please help me how to fix this issue?
>>
>
> Which atoms are in that interaction on that line, and should there be such
> an interaction there?
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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[gmx-users] Energy analysis

[Amir Zeb]

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 follow a specific
tutorial?

Amir
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Re: [gmx-users] Energy analysis

[Amir Zeb]

Yes Dr. Dallas,

I have gone through free energy analysis tutorial, But I'm wondering that
whether this tutorial is working for large molecule like protein or not?
Because the tutorial has explained methane only.
Your feedback will highly be appreciated.

Thanks!

Amir

On Sun, Nov 19, 2017 at 5:54 PM, Dallas Warren <dallas.war...@monash.edu>
wrote:

> Always a good starting point 
>
> http://www.gromacs.org/Documentation/Tutorials
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 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 <zebami...@gmail.com> wrote:
> > Thanks Mark,
> >
> > Depends what you mean by "stability."
> > Actually, I don't know the role of metal ion if it is used as co-factor
> by
> > a particular protein. I thought to do comparative analysis by MD
> simulation
> > which might predict the possible role of metal (in this case Zn^2+).
> Other
> > analysis like RMSD, RMSF, Rg, SASA, and structural analysis etc. I have
> > already done, but I want to get insight in their energetic terms while
> > addressing the question why such changes occurred?
> > According to the best of my study, there is no experimental data
> available
> > for my target protein and that's why I want to predict its free-energy of
> > folding or whatever else.
> > Will you kindly suggest me some hand notes or tutorial like to do
> > free-energy analysis for both the systems; means a) protein with metal
> ion
> > and b) protein without metal ion?
> >
> > Amir
> >
> > On Sun, Nov 19, 2017 at 11:32 AM, Mark Abraham <mark.j.abra...@gmail.com
> >
> > wrote:
> >
> >> Hi,
> >>
> >> Depends what you mean by "stability." A well designed study could seek
> to
> >> measure or estimate the difference in the free-energy of folding, but
> that
> >> would probably require an infeasibly large amount of sampling, and be
> >> highly dependent on the quality 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 <zebami...@gmail.com> wrote:
> >>
> >> > 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 follow a specific
> >> > tutorial?
> >> >
> >> > Amir
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> > posting!
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> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
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> >> >
> >> --
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Re: [gmx-users] Energy analysis

[Amir Zeb]

Thanks Mark,

Depends what you mean by "stability."
Actually, I don't know the role of metal ion if it is used as co-factor by
a particular protein. I thought to do comparative analysis by MD simulation
which might predict the possible role of metal (in this case Zn^2+). Other
analysis like RMSD, RMSF, Rg, SASA, and structural analysis etc. I have
already done, but I want to get insight in their energetic terms while
addressing the question why such changes occurred?
According to the best of my study, there is no experimental data available
for my target protein and that's why I want to predict its free-energy of
folding or whatever else.
Will you kindly suggest me some hand notes or tutorial like to do
free-energy analysis for both the systems; means a) protein with metal ion
and b) protein without metal ion?

Amir

On Sun, Nov 19, 2017 at 11:32 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Depends what you mean by "stability." A well designed study could seek to
> measure or estimate the difference in the free-energy of folding, but that
> would probably require an infeasibly large amount of sampling, and be
> highly dependent on the quality 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 <zebami...@gmail.com> wrote:
>
> > 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 follow a specific
> > tutorial?
> >
> > Amir
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Distances calculation in umbrella sampling

[Amir Zeb]

Hi
Replace the name of groups in original script by the names in between which
you want to measure the distance

Good luck!

On Dec 1, 2017 5:50 PM, "Kingsley Theras Primus Dass ." <
105726...@gms.tcu.edu.tw> wrote:

> dear users,
>  I am encountering a problem with script, the summary.dat file does
> not generate
> any value. But if I run the distance command one at the time , it is
> generating the value, I could not figure out where I am goingperlgmx wrong.
> can anyone tell where lies the mistake?mistake?
>
>
> Thank you
>
> *below the command line for one distance *
> Command line:
>   gmx_mpi distance -s sgdp_pull_t.tpr -f conf1.pdb -n index.ndx -oall
> dist1.xvgtpr -f conf1.pdb -n index.ndx -oall dist1.xvg -n index. -
> dist1.xvg
> pdbndxoall
>
> Available static index groups:
>  Group 0 "System" (89993 atoms)
>  Group 1 "Protein" (6541 atoms)
>  Group 2 "Protein-H" (5087 atoms)
>  Group 3 "C-alpha" (644 atoms)
>  Group 4 "Backbone" (1932 atoms)
>  Group 5 "MainChain" (2578 atoms)
>  Group 6 "MainChain + Cb" (3192 atoms)
>  Group 7 "MainChain + H" (3209 atoms)
>  Group 8 "SideChain" (3332 atoms)
>  Group 9 "SideChain-H" (2509 atoms)
>  Group 10 "Prot-Masses" (6541 atoms)
>  Group 11 "non-Protein" (83452 atoms)
>  Group 12 "Other" (12949 atoms)
>  Group 13 "_ *" (19 atoms)
>  Group 14 "GDP" (34 atoms)
>  Group 15 "POPC" (12896 atoms)
>  Group 16 "NA" (107 atoms)
>  Group 17 "CL" (106 atoms)
>  Group 18 "Water" (70290 atoms)
>  Group 19 "SOL" (70290 atoms)
>  Group 20 "non-Water" (19703 atoms)
>  Group 21 "Ion" (213 atoms)
>  Group 22 "_ *" (19 atoms)
>  Group 23 "GDP" (34 atoms)
>  Group 24 "POPC" (12896 atoms)
>  Group 25 "NA" (107 atoms)
>  Group 26 "CL" (106 atoms)
>  Group 27 "Water_and_ions" (70503 atoms)
>  Group 28 "Protein_chain_A" (3536 atoms)
> Specify any number of selections for option 'select'
> (Position pairs to calculate distances for):
> (one per line,  for status / groups, 'help' for help, Ctrl-D to end)
>
> > Reading file sgdp_pull_t.tpr, VERSION 5.1.4 (single precision)
> Reading file sgdp_pull_t.tpr, VERSION 5.1.4 (single precision)
> Reading frame 0 time 10.000 '', 89993 atoms
> Last frame 0 time 10.000
> Analyzed 1 frames, last time 0.000
> GDP:
>   Number of samples: 17
>   Average distance: 0.16202 nm
>   Standard deviation: 0.05626 nm
> Protein_chain_A:
>   Number of samples: 1768
>   Average distance: 0.19869 nm
>   Standard deviation: 0.12505 nm
>
>
>
> the error message that I get when I run perl script perl script
>
> 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 concatenation (.) Or string at
> distances.pl line 30.
> 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 concatenation (.) Or string at
> distances.pl line 30.
> 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 concatenation (.) Or string at
> distances.pl line 30.
> 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 concatenation (.) Or string at
> distances.pl line 30.
> 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 concatenation (.) Or string at
> distances.pl line 30.
> Cleaning up ...
>
>
>
> 2017-11-30 23:10 GMT+08:00 Amir Zeb <zebami...@gmail.com>:
>
> > Solved it,
> >
> > Thanks every one!
> >
> > Amir
> >
> > On Thu, Nov 30, 2017 at 5:06 AM, Justin Lemkul <jalem

[gmx-users] Problem with topology generation by Amber 12 ff

[Amir Zeb]

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 such error. I
searched out the solution on google but could not find the answer.

Please help me how to fix this issue?

Thanks in advance!
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[gmx-users] S-nitrosoylated proteins

[Amir Zeb]

Hello folks,

Which force field has parameters for S-nitrosoylated cysteine?
How may I get it?

Thanks!

Amir
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[gmx-users] Issue regarding MN+2

[Amir Zeb]

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 ]
; Namenrexcl
Other_chain_C2  3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
  chargeB  massB
; residue 501 MN2  rtp MN   q +2.0
 1MN 501MN2  MN  1  2  54.94   ;
qtot 2
; residue 502 MN2  rtp MN   q +2.0
 2MN 502MN2  MN  2  2  54.94   ;
qtot 4


And the Mn+2 has this configuration:

  501MN2 MN 4551   5.405   5.564   2.987
  502MN2 MN 4552   5.582   5.590   3.497

I have used Charmm36 ff, and the gromacs version is 5.0.6

Please let me know how can I fix this issue?

~Amir
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Re: [gmx-users] Issue regarding MN+2

[Amir Zeb]

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" <jalem...@vt.edu> wrote:

>
>
> On 12/29/17 10:11 AM, Amir Zeb wrote:
>
>> 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 ]
>> ; Namenrexcl
>> Other_chain_C2  3
>>
>> [ atoms ]
>> ;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
>>chargeB  massB
>> ; residue 501 MN2  rtp MN   q +2.0
>>   1MN 501MN2  MN  1  2  54.94   ;
>> qtot 2
>> ; residue 502 MN2  rtp MN   q +2.0
>>   2MN 502MN2  MN  2  2  54.94   ;
>> qtot 4
>>
>>
>> And the Mn+2 has this configuration:
>>
>>501MN2 MN 4551   5.405   5.564   2.987
>>502MN2 MN 4552   5.582   5.590   3.497
>>
>> I have used Charmm36 ff, and the gromacs version is 5.0.6
>>
>> Please let me know how can I fix this issue?
>>
>
> This is not a standard CHARMM atom type - did you add it yourself? If so,
> what was the source of the parameters? It looks like you have a residue
> defined in the .rtp, hence pdb2gmx wrote the topology, but you don't
> actually have parameters assigned for the atom type in ffnonbonded.itp.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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>
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Re: [gmx-users] Issue regarding MN+2

[Amir Zeb]

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 <jalem...@vt.edu> wrote:

>
>
> On 12/29/17 10:39 AM, Amir Zeb wrote:
>
>> Thanks Dr. Justin.
>>
>> I didn't add this stuff by my own.
>> I have created Mn+2 topology by simple pdb2gmx command.
>>
>
> Someone hacked your files and added it at some point. None of the releases
> of the C36 port that I have ever made had contained Mn2+ parameters. There
> are CHARMM-compatible parameters that could be added as part of a larger
> metal parameter set, but they've never been included in the port.
>
> Regardless, that's what you need to do - add the correct sigma and epsilon
> values to ffnonbonded.itp for the MN atom type.
>
> -Justin
>
>
> ~Amir
>>
>> On Dec 30, 2017 12:21 AM, "Justin Lemkul" <jalem...@vt.edu> wrote:
>>
>>
>>> On 12/29/17 10:11 AM, Amir Zeb wrote:
>>>
>>> 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 ]
>>>> ; Namenrexcl
>>>> Other_chain_C2  3
>>>>
>>>> [ atoms ]
>>>> ;   nr   type  resnr residue  atom   cgnr charge   mass
>>>> typeB
>>>> chargeB  massB
>>>> ; residue 501 MN2  rtp MN   q +2.0
>>>>1MN 501MN2  MN  1  2  54.94
>>>>  ;
>>>> qtot 2
>>>> ; residue 502 MN2  rtp MN   q +2.0
>>>>2MN 502MN2  MN  2  2  54.94
>>>>  ;
>>>> qtot 4
>>>>
>>>>
>>>> And the Mn+2 has this configuration:
>>>>
>>>> 501MN2 MN 4551   5.405   5.564   2.987
>>>> 502MN2 MN 4552   5.582   5.590   3.497
>>>>
>>>> I have used Charmm36 ff, and the gromacs version is 5.0.6
>>>>
>>>> Please let me know how can I fix this issue?
>>>>
>>>> This is not a standard CHARMM atom type - did you add it yourself? If
>>> so,
>>> what was the source of the parameters? It looks like you have a residue
>>> defined in the .rtp, hence pdb2gmx wrote the topology, but you don't
>>> actually have parameters assigned for the atom type in ffnonbonded.itp.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> 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 (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
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>
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Re: [gmx-users] Error regarding pdb2gmx of modified residue

[Amir Zeb]

Thanks Mark,

Actually, the pdb file which I'm trying to execute for topology generation,
has one residue (TYR15) is modified to phosphorylated tyrosine. Once I'm
directing to command prompt for selection of termini, N-terminus is fine
where it is needed for GLN-2, but the app asking C-terminus for THR-14
which lies before TYR-15 (in this case TP2-15 which is explained in
aforementioned email). I will attach the snap right here to let you clear
the query.

Select start terminus type for GLN-2
 0: NH3+
 1: NH2
 2: 5TER
 3: None
0
Start terminus GLN-2: NH3+
Select end terminus type for THR-14
 0: COO-
 1: COOH
 2: CT2
 3: 3TER
 4: None
0
End terminus THR-14: COO-
Opening force field file ./charmm36-jul2017.ff/merged.arn

So, I don't why am I getting this comment? The C-terminal residue of my pdb
file is SER-287. Please let me know if possible why C-terminus is needed
for THR-14 of the pdb file? If you kindly need more information, I will go
through.

Also, some has faced the similar issue here:

https://www.researchgate.net/post/How_can_I_prevent_GROMACS_50_with_CHARMM36_from_wrongly_identifying_the_residue_preceding_a_phosphorylated_amino_acid_as_a_C-terminal


But I couldn't follow, how to resolve it?

Thanks!

~Amir

On Mon, Jan 1, 2018 at 9:58 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> I would rename those atoms exactly as the .tdb file in your force field
> expects. And if that doesn't work, try deleting them and having pdb2gmx
> rebuild them.
>
> Mark
>
> On Mon, Jan 1, 2018 at 5:53 AM Amir Zeb <zebami...@gmail.com> 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 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- as C-terminus
> > TIP3P water model
> >
> > I am getting error:
> >
> > Fatal error:
> > Atom OXT in residue SER 287 was not found in rtp entry SER with 11 atoms
> > while sorting atoms.
> >
> > The C-terminus of my pdb file is pasted right here:
> > ATOM   4538  OC1 SER A 287
> > ATOM   4539  OC2 SER A 287
> > TER  4540   SER A 287
> > END
> >
> > I am aware of that SER 287 is C-terminus residue but by which name
> should i
> > replace the terminal oxygen to cope with this error?
> >
> > Looking forward for your kind suggestions.
> >
> > Thanks in advance!
> >
> > ~Amir
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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Re: [gmx-users] Error regarding pdb2gmx of modified residue

[Amir Zeb]

Alright Mark,

pdb2gmx does not give me output file in complete, it crashes before the
generation of top and gro files for the protein, while generating the above
mentioned fatal error.

~Amir

On Mon, Jan 1, 2018 at 11:21 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Just as Justin said there, 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 AM Amir Zeb <zebami...@gmail.com> wrote:
>
> > Thanks Mark,
> >
> > Actually, the pdb file which I'm trying to execute for topology
> generation,
> > has one residue (TYR15) is modified to phosphorylated tyrosine. Once I'm
> > directing to command prompt for selection of termini, N-terminus is fine
> > where it is needed for GLN-2, but the app asking C-terminus for THR-14
> > which lies before TYR-15 (in this case TP2-15 which is explained in
> > aforementioned email). I will attach the snap right here to let you clear
> > the query.
> >
> > Select start terminus type for GLN-2
> >  0: NH3+
> >  1: NH2
> >  2: 5TER
> >  3: None
> > 0
> > Start terminus GLN-2: NH3+
> > Select end terminus type for THR-14
> >  0: COO-
> >  1: COOH
> >  2: CT2
> >  3: 3TER
> >  4: None
> > 0
> > End terminus THR-14: COO-
> > Opening force field file ./charmm36-jul2017.ff/merged.arn
> >
> > So, I don't why am I getting this comment? The C-terminal residue of my
> pdb
> > file is SER-287. Please let me know if possible why C-terminus is needed
> > for THR-14 of the pdb file? If you kindly need more information, I will
> go
> > through.
> >
> > Also, some has faced the similar issue here:
> >
> >
> > https://www.researchgate.net/post/How_can_I_prevent_
> GROMACS_50_with_CHARMM36_from_wrongly_identifying_the_residue_preceding_a_
> phosphorylated_amino_acid_as_a_C-terminal
> >
> >
> > But I couldn't follow, how to resolve it?
> >
> > Thanks!
> >
> > ~Amir
> >
> > On Mon, Jan 1, 2018 at 9:58 PM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > I would rename those atoms exactly as the .tdb file in your force field
> > > expects. And if that doesn't work, try deleting them and having pdb2gmx
> > > rebuild them.
> > >
> > > Mark
> > >
> > > On Mon, Jan 1, 2018 at 5:53 AM Amir Zeb <zebami...@gmail.com> 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 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- as C-terminus
> > > > TIP3P water model
> > > >
> > > > I am getting error:
> > > >
> > > > Fatal error:
> > > > Atom OXT in residue SER 287 was not found in rtp entry SER with 11
> > atoms
> > > > while sorting atoms.
> > > >
> > > > The C-terminus of my pdb file is pasted right here:
> > > > ATOM   4538  OC1 SER A 287
> > > > ATOM   4539  OC2 SER A 287
> > > > TER  4540   SER A 287
> > > > END
> > > >
> > > > I am aware of that SER 287 is C-terminus residue but by which name
> > > should i
> > > > replace the terminal oxygen to cope with this error?
> > > >
> > > > Looking forward for your kind suggestions.
> > > >
> > > > Thanks in advance!
> > > >
> > > > ~Amir
> > > > --
> > > > 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 (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
&

[gmx-users] Error regarding pdb2gmx of modified residue

[Amir Zeb]

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- as C-terminus
TIP3P water model

I am getting error:

Fatal error:
Atom OXT in residue SER 287 was not found in rtp entry SER with 11 atoms
while sorting atoms.

The C-terminus of my pdb file is pasted right here:
ATOM   4538  OC1 SER A 287
ATOM   4539  OC2 SER A 287
TER  4540   SER A 287
END

I am aware of that SER 287 is C-terminus residue but by which name should i
replace the terminal oxygen to cope with this error?

Looking forward for your kind suggestions.

Thanks in advance!

~Amir
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Re: [gmx-users] Issue regarding MN+2

[Amir Zeb]

Thanks Dr. Justin,

Let me try.

~Amir

On Sat, Dec 30, 2017 at 8:14 AM, Justin Lemkul <jalem...@vt.edu> 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't included in the port?
>> I'm searching the literature too to find something worthy.
>>
>
> The parameters that we consider compatible with CHARMM are
> dx.doi.org/10.1021/jp309150r
>
> We have used them recently in a protein that coordinates Mn2+ via His,
> which requires additional bonded parameters for proper coordination, see
> https://doi.org/10.1128/AAC.01572-17 (parameters in the SI).
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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[gmx-users] Residue not found in topology

[Amir Zeb]

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/src/gromacs/gmxpreprocess/resall.c,
line: 645

Fatal error:
Residue 'KAC' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Is CharmM 36 ff capable to simulate modified residue acetylated lysine?
If yes, what is the ff compatible notation for acetylated lysine?
If not, which ff can I use to simulate acetylated lysine?

Thanks in advance!

Amir
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Re: [gmx-users] Residue not found in topology

[Amir Zeb]

Thanks Justin,

Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/  and
generated the parameters for KAC.
The merged.rtp file was modified by adding the KAC parameters
That issue fixed, but now I'm getting the following warning which
ultimately results in fatal error.

WARNING: atom HA is missing in residue KAC 33 in the pdb file
 You might need to add atom HA to the hydrogen database of building
block KAC
 in the file merged.hdb (see the manual)


WARNING: atom HB1 is missing in residue KAC 33 in the pdb file
 You might need to add atom HB1 to the hydrogen database of
building block KAC
 in the file merged.hdb (see the manual)


WARNING: atom HB2 is missing in residue KAC 33 in the pdb file
 You might need to add atom HB2 to the hydrogen database of
building block KAC
 in the file merged.hdb (see the manual)


WARNING: atom HG1 is missing in residue KAC 33 in the pdb file
 You might need to add atom HG1 to the hydrogen database of
building block KAC
 in the file merged.hdb (see the manual)


WARNING: atom HG2 is missing in residue KAC 33 in the pdb file
 You might need to add atom HG2 to the hydrogen database of
building block KAC
 in the file merged.hdb (see the manual)


WARNING: atom HD1 is missing in residue KAC 33 in the pdb file
 You might need to add atom HD1 to the hydrogen database of
building block KAC
 in the file merged.hdb (see the manual)


WARNING: atom HD2 is missing in residue KAC 33 in the pdb file
 You might need to add atom HD2 to the hydrogen database of
building block KAC
 in the file merged.hdb (see the manual)


WARNING: atom HE1 is missing in residue KAC 33 in the pdb file
 You might need to add atom HE1 to the hydrogen database of
building block KAC
 in the file merged.hdb (see the manual)


WARNING: atom HE2 is missing in residue KAC 33 in the pdb file
 You might need to add atom HE2 to the hydrogen database of
building block KAC
 in the file merged.hdb (see the manual)


WARNING: atom HZ1 is missing in residue KAC 33 in the pdb file
 You might need to add atom HZ1 to the hydrogen database of
building block KAC
 in the file merged.hdb (see the manual)


WARNING: atom HI11 is missing in residue KAC 33 in the pdb file
 You might need to add atom HI11 to the hydrogen database of
building block KAC
 in the file merged.hdb (see the manual)


WARNING: atom HI12 is missing in residue KAC 33 in the pdb file
 You might need to add atom HI12 to the hydrogen database of
building block KAC
 in the file merged.hdb (see the manual)


WARNING: atom HI13 is missing in residue KAC 33 in the pdb file
 You might need to add atom HI13 to the hydrogen database of
building block KAC
 in the file merged.hdb (see the manual)


WARNING: atom HZ2 is missing in residue KAC 33 in the pdb file
 You might need to add atom HZ2 to the hydrogen database of
building block KAC
 in the file merged.hdb (see the manual)


WARNING: atom HT2 is missing in residue KAC 33 in the pdb file
 You might need to add atom HT2 to the hydrogen database of
building block KAC
 in the file merged.hdb (see the manual)

How may I fix this issue?

Thanks in advance!


On Wed, Aug 22, 2018 at 4:31 AM Justin Lemkul  wrote:

>
>
> On 8/22/18 5:26 AM, Bratin Kumar Das wrote:
> > Hi
> >  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.
>
> The error has nothing to do with grompp. The topology was never created
> because pdb2gmx could not write a topology for KAC.
>
> CHARMM36 does support KAC, but not as a standalone residue. In CHARMM,
> one would generate a normal lysine then patch it with the KAC patch. To
> make this work in GROMACS, one would have to create a KAC .rtp entry by
> applying the same logic - modify LYS according to the KAC patch (found
> in the stream/prot/toppar_all36_prot_modify_res.str file from the
> tarball distributed by Alex MacKerell:
> http://mackerell.umaryland.edu/charmm_ff.shtml#charmm).
>
> -Justin
>
> > On Wed 22 Aug, 2018, 2:53 PM Bratin Kumar Das, <
> 177cy500.bra...@nitk.edu.in>
> > wrote:
> >
> >> Hi
> >>  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 wa

Re: [gmx-users] Residue not found in topology

[Amir Zeb]

Thanks Justin,
I have followed what did you suggest for .rtp entry in merged.rtp file of
charmm36 ff.
But i could not make .hdb file for ALY. Where can i find the H-information
for ALY to insert them in merged.hdb file of charmm36 ff?

Amir

On Thu, Aug 23, 2018, 9:02 PM Justin Lemkul  wrote:

>
>
> On 8/23/18 7:52 AM, Bratin Kumar Das wrote:
> > Hi
> > You can see that only the problem is coming from hydrogen. So in
> pdb2gmx
> > command use -ignh so that it ignores the hydrogen. If you use this this
> > WARNING will not come.
>
> That's not 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 built.
>
> -Justin
>
> > On Fri, Aug 24, 2018 at 4:00 AM, Amir Zeb  wrote:
> >
> >> Thanks Justin,
> >>
> >> Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/
> and
> >> generated the parameters for KAC.
> >> The merged.rtp file was modified by adding the KAC parameters
> >> That issue fixed, but now I'm getting the following warning which
> >> ultimately results in fatal error.
> >>
> >> WARNING: atom HA is missing in residue KAC 33 in the pdb file
> >>   You might need to add atom HA to the hydrogen database of
> building
> >> block KAC
> >>   in the file merged.hdb (see the manual)
> >>
> >>
> >> WARNING: atom HB1 is missing in residue KAC 33 in the pdb file
> >>   You might need to add atom HB1 to the hydrogen database of
> >> building block KAC
> >>   in the file merged.hdb (see the manual)
> >>
> >>
> >> WARNING: atom HB2 is missing in residue KAC 33 in the pdb file
> >>   You might need to add atom HB2 to the hydrogen database of
> >> building block KAC
> >>   in the file merged.hdb (see the manual)
> >>
> >>
> >> WARNING: atom HG1 is missing in residue KAC 33 in the pdb file
> >>   You might need to add atom HG1 to the hydrogen database of
> >> building block KAC
> >>   in the file merged.hdb (see the manual)
> >>
> >>
> >> WARNING: atom HG2 is missing in residue KAC 33 in the pdb file
> >>   You might need to add atom HG2 to the hydrogen database of
> >> building block KAC
> >>   in the file merged.hdb (see the manual)
> >>
> >>
> >> WARNING: atom HD1 is missing in residue KAC 33 in the pdb file
> >>   You might need to add atom HD1 to the hydrogen database of
> >> building block KAC
> >>   in the file merged.hdb (see the manual)
> >>
> >>
> >> WARNING: atom HD2 is missing in residue KAC 33 in the pdb file
> >>   You might need to add atom HD2 to the hydrogen database of
> >> building block KAC
> >>   in the file merged.hdb (see the manual)
> >>
> >>
> >> WARNING: atom HE1 is missing in residue KAC 33 in the pdb file
> >>   You might need to add atom HE1 to the hydrogen database of
> >> building block KAC
> >>   in the file merged.hdb (see the manual)
> >>
> >>
> >> WARNING: atom HE2 is missing in residue KAC 33 in the pdb file
> >>   You might need to add atom HE2 to the hydrogen database of
> >> building block KAC
> >>   in the file merged.hdb (see the manual)
> >>
> >>
> >> WARNING: atom HZ1 is missing in residue KAC 33 in the pdb file
> >>   You might need to add atom HZ1 to the hydrogen database of
> >> building block KAC
> >>   in the file merged.hdb (see the manual)
> >>
> >>
> >> WARNING: atom HI11 is missing in residue KAC 33 in the pdb file
> >>   You might need to add atom HI11 to the hydrogen database of
> >> building block KAC
> >>   in the file merged.hdb (see the manual)
> >>
> >>
> >> WARNING: atom HI12 is missing in residue KAC 33 in the pdb file
> >>   You might need to add atom HI12 to the hydrogen database of
> >> building block KAC
> >>   in the file merged.hdb (see the manual)
> >>
> >>
> >> WARNING: atom HI13 is missing in residue KAC 33 in the pdb file
> >>   You might need to add atom HI13 to the hydrogen database of
> >> build