Re: [gmx-users] QM-MM (sai manohar)

[sai manohar]

Thank you for the guidance. I shall browse through for other alternatives.
:)

On Mon, May 28, 2018 at 6:14 PM, Groenhof, Gerrit  wrote:

> Hi,
>
> Unfortunately,  for this to work
> you need to have both heme and protein in one topology.
>
> best,
>
> gerrit
>
> Tidings and a good day.
>
> Hi,
>
> I'm looking at a QM-MM/Gromacs optimization for a Heme-CYP system. How do I
> take it forward. I've found one strategy using a dummy atom in linker.
> However, there's a small issue in this route. How do we incorporate the
> dummy if the link we are pursuing is between the protein and the Heme that
> are processed into two separate .top files in the first gmx step of
> protein_proc.gro?
>
> Any guidance in this direction would be extremely helpful.
>
>
> Thank you.
>
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Re: [gmx-users] Regarding calculation of SDF

[Dallas Warren]

What exactly is the issue?  It isn't clear what the problem is; the
fact it is having trouble with using the tng file format, or the
output in the cube file that is then loaded into vmd?
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 28 May 2018 at 12:17, Dilip.H.N  wrote:
> Hi,
> I want to calculate the Spatial Distribution Function of say N-terminal
> nitrogen atom and all the oxygen atoms of the water molecules.
> So, i have created the index file in which i have the nitrogen atom and all
> the oxygen atoms of water molecules. And here are my commands that i gave
> inorder to calculate SDF:
> gmx trjconv -s nptmd.tpr -f nptmd.xtc -n ndx_NOw.ndx -o abc.tng -ur compact
> -pbc whole
> gmx trjconv -s nptmd.tpr -f abc.tng -n ndx_NOw.ndx -o def.tng -fit rot+trans
> gmx spatial -s nptmd.tpr -n ndx_NOw.ndx -f def.tng -nab 10
>
> I get the following:
> Reading file nptmd.tpr, VERSION 2016.2 (single precision)
> Select group to generate SDF:
> Group 0 ( N) has 1 elements
> Group 1 ( OW) has   511 elements
> Select a group: 0
> Selected 0: 'N'
> Select group to output coords (e.g. solute):
> Group 0 ( N) has 1 elements
> Group 1 ( OW) has   511 elements
> Select a group: 1
> Selected 1: 'OW'
> TNG library: Cannot uncompress data block.
> /home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c:
> 5298
> TNG library: Cannot uncompress data block.
> /home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c:
> 5298
> Last frame  6 time 3.000
> Back Off! I just backed up grid.cube to ./#grid.cube.1#
> Counts per frame in all 27 cubes divided by 3.703704e-02
> Normalized data: average 1.00e+00, min 0.00e+00, max 2.70e+01
>
>
> and if i view the grid.cube file in vmd, i am unable to get a proper SDF/it
> is wired when i give an isovalues and change its values...
>
> How can i solve this..??
> Any suggestions are highly appreciated.
>
> Thank you.
>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
> [image: Mailtrack]
> 
> Sender
> notified by
> Mailtrack
> 
> 05/28/18,
> 7:47:09 AM
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Re: [gmx-users] AMP_simulation

[Dallas Warren]

The ATB generator does a reasonable job, but for some reason it gets
some things wrong.  If you can look at that topology, identify the
problematic parts of it, see if that is consistent with the
forcefield, and then if not adjust the parameters.  Particularly I
have found that some angles are way too large, giving fast moving bond
angles, which then become unstable.
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 24 May 2018 at 22:01,   wrote:
> Hello,
>
> I have tried doing the Molecular dynamics simulation of AMP using the
> Gromos54a7 forcefield.
>
> ITP parameters for the AMP molecule has been generated using the ATB
> builder. Minimization of the molecule goes on well however while carrying
> out the Nvt theres a segmantation fault resulting in step files.
>
> Moreover LINCS warning are shown with bonds that rotated more than 30
> degrees. ihave tried changing lincs parameter and also increasing the step
> size, but still simulation crashes.
>
> Is it suggestible to generate topology for the AMP molecule from the
> available topological parameters of ATP in GROMACS. Or are their any
> source of getting the correct itp paremeters for "AMP".
>
> Thanks
> Nikita Bora
>
>
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Re: [gmx-users] velocity

[Quyen V. Vu]

Maybe you checked .xtc file
Velocity is in .trr file

Quyen V. Vu

Web frontend developer

On Mon, May 28, 2018, 18:42 Mark Abraham  wrote:

> Hi,
>
> Only if you asked for velocity information to be written to the trajectory,
> with nstvout
>
> Mark
>
> On Mon, May 28, 2018 at 1:06 PM Atila Petrosian  >
> wrote:
>
> > Dear gromacs users,
> >
> > I did md simulation. I need to velocity values for each atoms in time
> > steps.
> >
> > Can I get this parameter from trajectory file directly?
> >
> > How to obtain that?
> >
> > Thanks
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Re: [gmx-users] md simulation of oil hydrocarbon

[Ali Ahmed]

for liquids use oplsaa

On Mon, May 28, 2018 at 12:23 PM, Atila Petrosian  wrote:

> Hi all,
>
> I want to do md simulation of oil hydrocarbon?
>
> Is there appropriate force field for these hydrocarbons in gromacs?
>
> What I see in gromacs force fields only was related to aminoacids and
> nucleotides.
>
> What is your suggestion for md simulation of oil hydrocarbon?
>
> Best,
> --
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[gmx-users] md simulation of oil hydrocarbon

[Atila Petrosian]

Hi all,

I want to do md simulation of oil hydrocarbon?

Is there appropriate force field for these hydrocarbons in gromacs?

What I see in gromacs force fields only was related to aminoacids and
nucleotides.

What is your suggestion for md simulation of oil hydrocarbon?

Best,
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[gmx-users] velocity

[Atila Petrosian]

Dear Mark and Justin,

My problem was solved using trr file.

Thanks for guidance.
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Re: [gmx-users] velocity

[Mark Abraham]

Hi,

An xtc file only contains positions. Your nstvout affects the trr file.
Notice how sharing your command line got you the answer you needed ;-)

Mark

On Mon, May 28, 2018, 18:12 Atila Petrosian 
wrote:

> Dear Justin,
>
> In my last md simulation, I used
>
> nstxout = 1000
> nstvout = 1000
> nstxtcout = 1000
> nstenergy = 1000
> nstlog = 1000
>
> After your suggestion, I used gmx traj -f npt.xtc -s npt.tpr  -ov veloc.xvg
> -n index.ndx
>
> veloc.xvg file is as follows:
>
> -
>
> @title "Velocity"
> @xaxis  label "Time (ps)"
> @yaxis  label "Velocity (nm/ps)"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "atom 1 X"
> @ s1 legend "atom 1 Y"
> @ s2 legend "atom 1 Z"
> .
> .
> .
> @ s2838 legend "atom 947 X"
> @ s2839 legend "atom 947 Y"
> @ s2840 legend "atom 947 Z"*** (last line of file) ***
>
> --
>
> There is no velocity values. Is my manner wrong?
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[gmx-users] velocity

[Atila Petrosian]

Dear Justin,

In my last md simulation, I used

nstxout = 1000
nstvout = 1000
nstxtcout = 1000
nstenergy = 1000
nstlog = 1000

After your suggestion, I used gmx traj -f npt.xtc -s npt.tpr  -ov veloc.xvg
-n index.ndx

veloc.xvg file is as follows:

-

@title "Velocity"
@xaxis  label "Time (ps)"
@yaxis  label "Velocity (nm/ps)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "atom 1 X"
@ s1 legend "atom 1 Y"
@ s2 legend "atom 1 Z"
.
.
.
@ s2838 legend "atom 947 X"
@ s2839 legend "atom 947 Y"
@ s2840 legend "atom 947 Z"*** (last line of file) ***

--

There is no velocity values. Is my manner wrong?
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Re: [gmx-users] velocity

[Justin Lemkul]

On 5/28/18 11:49 AM, Atila Petrosian wrote:

Dear Mark,
Thanks for your answer.

"Only if you asked for velocity information to be written to the
trajectory, with nstvout"

Usually, I use the following lines in mdp files:

nstxout = 1000
nstvout = 1000
nstxtcout = 1000
nstenergy = 1000
nstlog = 1000

But, I get only position of atoms  in time steps using VMD while I need to
the velocity values for each time in time steps.


Inspect the contents of your .trr file to verify what you have (is what 
you "usually" do what you "always" do, or did you forget something in 
this case?) and then, if velocities are present, extract what you need 
with gmx traj.


-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.thelemkullab.com

==

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[gmx-users] velocity

[Atila Petrosian]

Dear Mark,
Thanks for your answer.

"Only if you asked for velocity information to be written to the
trajectory, with nstvout"

Usually, I use the following lines in mdp files:

nstxout = 1000
nstvout = 1000
nstxtcout = 1000
nstenergy = 1000
nstlog = 1000

But, I get only position of atoms  in time steps using VMD while I need to
the velocity values for each time in time steps.
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[gmx-users] md simulation of oil hydrocarbon?

[Atila Petrosian]

 Hi all,

I want to do md simulation of oil hydrocarbon?

Is there appropriate force field for these hydrocarbons in gromacs?

Is it possible with gromacs?

Best,
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Re: [gmx-users] Partial Charge precision

[Momin Ahmad]

Hi,

yeah i missed the charge group number. Thanks for reminding

Cheers,

Momin


Am 28.05.2018 um 16:59 schrieb Justin Lemkul:



On 5/28/18 10:34 AM, Momin Ahmad wrote:

Hello,
how many decimal digits are allowed in .rtp files for partial charges?

i got this error:

##
Using the Uff4mof force field in directory ./uff4mof.ff

No file 'watermodels.dat' found, will not include a water model
Reading benzene.pdb...
Read 'BENZENE', 12 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 1 residues with 12 atoms

  chain  #res #atoms
  1 ' ' 1 12

All occupancies are one
Opening force field file ./uff4mof.ff/atomtypes.atp

Invalid format: [ atomtypes ]
Atomtype 146
Reading residue database... (uff4mof)
Opening force field file ./uff4mof.ff/bb.rtp

---
Program: gmx pdb2gmx, version 2016.3
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 489)

Fatal error:
in .rtp file in residue BDC at line:
    C1        C_1        -0.0313981005
###

I wrote down the whole number and did not round anything.



That's way too many digits to have any practical use or meaning. I'd 
suggest rounding to -0.0314.


The error is about the format of the line, not the precision of the 
value, so your .rtp entry is broken in some way (perhaps simply due to 
the absence of a charge group number, but it could be one of several 
things).


-Justin



--
Momin Ahmad

Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: momin.ah...@kit.edu

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Re: [gmx-users] Partial Charge precision

[Justin Lemkul]

On 5/28/18 10:34 AM, Momin Ahmad wrote:

Hello,
how many decimal digits are allowed in .rtp files for partial charges?

i got this error:

##
Using the Uff4mof force field in directory ./uff4mof.ff

No file 'watermodels.dat' found, will not include a water model
Reading benzene.pdb...
Read 'BENZENE', 12 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 1 residues with 12 atoms

  chain  #res #atoms
  1 ' ' 1 12

All occupancies are one
Opening force field file ./uff4mof.ff/atomtypes.atp

Invalid format: [ atomtypes ]
Atomtype 146
Reading residue database... (uff4mof)
Opening force field file ./uff4mof.ff/bb.rtp

---
Program: gmx pdb2gmx, version 2016.3
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 489)

Fatal error:
in .rtp file in residue BDC at line:
    C1        C_1        -0.0313981005
###

I wrote down the whole number and did not round anything.



That's way too many digits to have any practical use or meaning. I'd 
suggest rounding to -0.0314.


The error is about the format of the line, not the precision of the 
value, so your .rtp entry is broken in some way (perhaps simply due to 
the absence of a charge group number, but it could be one of several 
things).


-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.thelemkullab.com

==

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[gmx-users] Partial Charge precision

[Momin Ahmad]

Hello,
how many decimal digits are allowed in .rtp files for partial charges?

i got this error:

##
Using the Uff4mof force field in directory ./uff4mof.ff

No file 'watermodels.dat' found, will not include a water model
Reading benzene.pdb...
Read 'BENZENE', 12 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 1 residues with 12 atoms

  chain  #res #atoms
  1 ' ' 1 12

All occupancies are one
Opening force field file ./uff4mof.ff/atomtypes.atp

Invalid format: [ atomtypes ]
Atomtype 146
Reading residue database... (uff4mof)
Opening force field file ./uff4mof.ff/bb.rtp

---
Program: gmx pdb2gmx, version 2016.3
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 489)

Fatal error:
in .rtp file in residue BDC at line:
    C1        C_1        -0.0313981005
###

I wrote down the whole number and did not round anything.

Cheers,
Momin

--
Momin Ahmad

Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: momin.ah...@kit.edu

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[gmx-users] (no subject)

[niki24]

Hello,

Can anyone provide me the topology for Adenosine Monophosphate Molecule
(AMP)for  Gromacs (gromos54a7 forcefield).

Thanks
Nikita Bora


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Re: [gmx-users] QM-MM (sai manohar)

[Groenhof, Gerrit]

Hi,

Unfortunately,  for this to work
you need to have both heme and protein in one topology. 

best,

gerrit

Tidings and a good day.

Hi,

I'm looking at a QM-MM/Gromacs optimization for a Heme-CYP system. How do I
take it forward. I've found one strategy using a dummy atom in linker.
However, there's a small issue in this route. How do we incorporate the
dummy if the link we are pursuing is between the protein and the Heme that
are processed into two separate .top files in the first gmx step of
protein_proc.gro?

Any guidance in this direction would be extremely helpful.


Thank you.

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Re: [gmx-users] velocity

[Mark Abraham]

Hi,

Only if you asked for velocity information to be written to the trajectory,
with nstvout

Mark

On Mon, May 28, 2018 at 1:06 PM Atila Petrosian 
wrote:

> Dear gromacs users,
>
> I did md simulation. I need to velocity values for each atoms in time
> steps.
>
> Can I get this parameter from trajectory file directly?
>
> How to obtain that?
>
> Thanks
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[gmx-users] velocity

[Atila Petrosian]

Dear gromacs users,

I did md simulation. I need to velocity values for each atoms in time steps.

Can I get this parameter from trajectory file directly?

How to obtain that?

Thanks
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Re: [gmx-users] calculation of distance between the center of geometry of two proteins

[SHAHEE ISLAM]

thank you so much for your reply.

On 5/28/18, Soham Sarkar  wrote:
>  use the latest .tpr formed after production run else try
>
> tpbconv -s dynamic.tpr -o dynamic_new.tpr
>
> On Mon, May 28, 2018 at 3:29 PM, SHAHEE ISLAM 
> wrote:
>
>> thank you so much.
>> after deleting from -select its now working.but the fatal error is
>> Molecule in topology has atom numbers below and above natoms (565).
>> You are probably trying to use a trajectory which does not match the
>> first 565 atoms of the run input file.
>> You can make a matching run input file with tpbconv.
>>
>>
>> On 5/28/18, SHAHEE ISLAM  wrote:
>> > after deleting -select
>> > this error is coming
>> > Invalid command line argument:
>> > cog of group "Chain_A" plus cog of group "Chain_B"
>> >
>> >
>> > On 5/28/18, Soham Sarkar  wrote:
>> >> Delete from -select.. previous are ok
>> >>
>> >> On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, 
>> wrote:
>> >>
>> >>> hi,
>> >>> to calculate the distance between the center of geometry of two
>> >>> proteins, i am using this command
>> >>> g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg
>> >>> -select 'cog of group "Chain_A" plus cog of group "Chain_B"'
>> >>> Invalid command line argument:
>> >>> -select
>> >>> here in this index file the two chain group name Chain_A and Chain_B
>> >>> how i will select the two chain.
>> >>>
>> >>> thanking you
>> >>> shahee islam
>> >>> university of calcutta
>> >>> --
>> >>> 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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>> >>
>> >> * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >> posting!
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>> send
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>> >>
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>
>
>
> --
> SOHAM SARKAR
> Junior Research Fellow
> Department of Chemistry
> INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
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[gmx-users] QM-MM

[sai manohar]

Tidings and a good day.

Hi,

I'm looking at a QM-MM/Gromacs optimization for a Heme-CYP system. How do I
take it forward. I've found one strategy using a dummy atom in linker.
However, there's a small issue in this route. How do we incorporate the
dummy if the link we are pursuing is between the protein and the Heme that
are processed into two separate .top files in the first gmx step of
protein_proc.gro?

Any guidance in this direction would be extremely helpful.


Thank you.
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Re: [gmx-users] calculation of distance between the center of geometry of two proteins

[Soham Sarkar]

 use the latest .tpr formed after production run else try

tpbconv -s dynamic.tpr -o dynamic_new.tpr

On Mon, May 28, 2018 at 3:29 PM, SHAHEE ISLAM  wrote:

> thank you so much.
> after deleting from -select its now working.but the fatal error is
> Molecule in topology has atom numbers below and above natoms (565).
> You are probably trying to use a trajectory which does not match the
> first 565 atoms of the run input file.
> You can make a matching run input file with tpbconv.
>
>
> On 5/28/18, SHAHEE ISLAM  wrote:
> > after deleting -select
> > this error is coming
> > Invalid command line argument:
> > cog of group "Chain_A" plus cog of group "Chain_B"
> >
> >
> > On 5/28/18, Soham Sarkar  wrote:
> >> Delete from -select.. previous are ok
> >>
> >> On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, 
> wrote:
> >>
> >>> hi,
> >>> to calculate the distance between the center of geometry of two
> >>> proteins, i am using this command
> >>> g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg
> >>> -select 'cog of group "Chain_A" plus cog of group "Chain_B"'
> >>> Invalid command line argument:
> >>> -select
> >>> here in this index file the two chain group name Chain_A and Chain_B
> >>> how i will select the two chain.
> >>>
> >>> thanking you
> >>> shahee islam
> >>> university of calcutta
> >>> --
> >>> 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.
> >>>
> >> --
> >> 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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-- 
SOHAM SARKAR
Junior Research Fellow
Department of Chemistry
INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
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Re: [gmx-users] calculation of distance between the center of geometry of two proteins

[Mark Abraham]

Hi,

g_dist does not take selection arguments so you cannot use -select or
anything that was an argument to it. You can either rely on the default
selections that all GROMACS tools make if there is no index file, or use
e.g. g_select to make an index file with the selections you want.

Note that gmx distance in more recent versions of GROMACS has the -select
keyword, which you should probably install and use :-)

Mark

On Mon, May 28, 2018, 11:55 SHAHEE ISLAM  wrote:

> after deleting -select
> this error is coming
> Invalid command line argument:
> cog of group "Chain_A" plus cog of group "Chain_B"
>
>
> On 5/28/18, Soham Sarkar  wrote:
> > Delete from -select.. previous are ok
> >
> > On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, 
> wrote:
> >
> >> hi,
> >> to calculate the distance between the center of geometry of two
> >> proteins, i am using this command
> >> g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg
> >> -select 'cog of group "Chain_A" plus cog of group "Chain_B"'
> >> Invalid command line argument:
> >> -select
> >> here in this index file the two chain group name Chain_A and Chain_B
> >> how i will select the two chain.
> >>
> >> thanking you
> >> shahee islam
> >> university of calcutta
> >> --
> >> 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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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] calculation of distance between the center of geometry of two proteins

[Soham Sarkar]

The command should be
g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg
Then select Chain_A and Chain_B as per the indexing number

On Mon, May 28, 2018 at 3:24 PM, SHAHEE ISLAM  wrote:

> after deleting -select
> this error is coming
> Invalid command line argument:
> cog of group "Chain_A" plus cog of group "Chain_B"
>
>
> On 5/28/18, Soham Sarkar  wrote:
> > Delete from -select.. previous are ok
> >
> > On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, 
> wrote:
> >
> >> hi,
> >> to calculate the distance between the center of geometry of two
> >> proteins, i am using this command
> >> g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg
> >> -select 'cog of group "Chain_A" plus cog of group "Chain_B"'
> >> Invalid command line argument:
> >> -select
> >> here in this index file the two chain group name Chain_A and Chain_B
> >> how i will select the two chain.
> >>
> >> thanking you
> >> shahee islam
> >> university of calcutta
> >> --
> >> 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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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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-- 
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Junior Research Fellow
Department of Chemistry
INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
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Re: [gmx-users] calculation of distance between the center of geometry of two proteins

[SHAHEE ISLAM]

thank you so much.
after deleting from -select its now working.but the fatal error is
Molecule in topology has atom numbers below and above natoms (565).
You are probably trying to use a trajectory which does not match the
first 565 atoms of the run input file.
You can make a matching run input file with tpbconv.


On 5/28/18, SHAHEE ISLAM  wrote:
> after deleting -select
> this error is coming
> Invalid command line argument:
> cog of group "Chain_A" plus cog of group "Chain_B"
>
>
> On 5/28/18, Soham Sarkar  wrote:
>> Delete from -select.. previous are ok
>>
>> On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM,  wrote:
>>
>>> hi,
>>> to calculate the distance between the center of geometry of two
>>> proteins, i am using this command
>>> g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg
>>> -select 'cog of group "Chain_A" plus cog of group "Chain_B"'
>>> Invalid command line argument:
>>> -select
>>> here in this index file the two chain group name Chain_A and Chain_B
>>> how i will select the two chain.
>>>
>>> thanking you
>>> shahee islam
>>> university of calcutta
>>> --
>>> 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.
>>>
>> --
>> 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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>> a
>> mail to gmx-users-requ...@gromacs.org.
>>
>
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Re: [gmx-users] calculation of distance between the center of geometry of two proteins

[SHAHEE ISLAM]

after deleting -select
this error is coming
Invalid command line argument:
cog of group "Chain_A" plus cog of group "Chain_B"


On 5/28/18, Soham Sarkar  wrote:
> Delete from -select.. previous are ok
>
> On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM,  wrote:
>
>> hi,
>> to calculate the distance between the center of geometry of two
>> proteins, i am using this command
>> g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg
>> -select 'cog of group "Chain_A" plus cog of group "Chain_B"'
>> Invalid command line argument:
>> -select
>> here in this index file the two chain group name Chain_A and Chain_B
>> how i will select the two chain.
>>
>> thanking you
>> shahee islam
>> university of calcutta
>> --
>> 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.
>>
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Re: [gmx-users] calculation of distance between the center of geometry of two proteins

[Soham Sarkar]

Delete from -select.. previous are ok

On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM,  wrote:

> hi,
> to calculate the distance between the center of geometry of two
> proteins, i am using this command
> g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg
> -select 'cog of group "Chain_A" plus cog of group "Chain_B"'
> Invalid command line argument:
> -select
> here in this index file the two chain group name Chain_A and Chain_B
> how i will select the two chain.
>
> thanking you
> shahee islam
> university of calcutta
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[gmx-users] calculation of distance between the center of geometry of two proteins

[SHAHEE ISLAM]

hi,
to calculate the distance between the center of geometry of two
proteins, i am using this command
g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg
-select 'cog of group "Chain_A" plus cog of group "Chain_B"'
Invalid command line argument:
-select
here in this index file the two chain group name Chain_A and Chain_B
how i will select the two chain.

thanking you
shahee islam
university of calcutta
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Re: [gmx-users] Colchicine topology

[Soham Sarkar]

Dear All,
   I have a simulation box of dimension 8*6*4 nm3. The center
of the box is the center of the two center of masses of two ss-DNA. I want
to calculate the 2D distribution of the ions surround the strands in the
box. I chose Chain_A, Chain_B and ion as three groups, rather I am confused
with the options that should be added to have the correct dimension of the
finally produced image. what argument I should add for -amax and -rmax?
Anything else I have to use in the command line? The colour is also not
shown , what is the reason? can anyone please tell me
Thanks in advance

On Mon, May 28, 2018 at 1:04 PM, Alex  wrote:

>
> That's not my intention - someone seeking a topology would do well to a)
>> know the past research to inform their decisions, including whether to
>> repeat deliberately, and b) also ask them to share input files.
>>
>> I was obviously joking, not to derail this thread. Besides, in
> biomolecular fields, FF development in general and topology building in
> particular, you guys have at least some unity in how to approach things. In
> solid state (or solid-liquid systems), we have a pretty arbitrary zoo. The
> cherry on top of this cake is recent OPLS-AA-based FF for two widely
> studied nanomaterials with partial charges coming from DDAP, which is
> entirely different from CHELPG used for OPLS originally. And everything
> fits everything!
>
>> A lot of past work is horrible, yes :-)
>>
>> Always!
>
> Alex
>
>
>
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>



-- 
SOHAM SARKAR
Junior Research Fellow
Department of Chemistry
INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
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[gmx-users] D Gsolv

[Gonzalez Fernandez, Cristina]

Dear Gromacs users,

Does anyone know the meaning of "D Gsolv" when you plot the area.xvg (output of 
g_sas)?



Any help will highly been appreciated.







Best,



C.

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Re: [gmx-users] g_sas

[András Ferenc WACHA]

Dear Cristina,

how did you call xmgrace? Did you supply the "-nxy" switch before
area.xvg or volume.xvg?

Regards,

Andras


On 05/28/2018 09:45 AM, Gonzalez Fernandez, Cristina wrote:
> Dear Gromacs users,
>
>
>
>
>
> I want to calculate the hydrophobic and hydrophilic area of a protein by 
> using the g_sas command. I have used:
>
> g_sas -f md.xtc -s md.tpr -o area.xvg -tv volume.xvg
>
>
>
> However, looking at the area.xvg with xmgrace, I can only see the hydrophobic 
> area not the hydrophilic. Besides, looking at the volume.xvg I can only see 
> the volume, not the density. Could anyone help me to see both hydrophobic and 
> hydrophilic area of my protein as well as its volume and density?
>
>
>
>
>
> Any help will highly been appreciated.
>
>
>
> Best,
>
> C.

-- 
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences
Hungarian Academy of Sciences (RCNS HAS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.mta.hu, 
CREDO SAXS instrument: http://credo.ttk.mta.hu




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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 169, Issue 96

[niki24]

> Send gromacs.org_gmx-users mailing list submissions to
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> Today's Topics:
>
>1. topology file (mostafa paknia)
>2. Re: topology file (Soham Sarkar)
>3. Re: topology file (Justin Lemkul)
>4. Regarding calculation of SDF (Dilip.H.N)
>5. Re: gromacs.org_gmx-users Digest, Vol 169, Issue 89
>   (nik...@tezu.ernet.in)
>
>
> --
>
> Message: 1
> Date: Sun, 27 May 2018 23:00:26 +0330
> From: mostafa paknia 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] topology file
> Message-ID:
>   

[gmx-users] g_sas

[Gonzalez Fernandez, Cristina]

Dear Gromacs users,





I want to calculate the hydrophobic and hydrophilic area of a protein by using 
the g_sas command. I have used:

g_sas -f md.xtc -s md.tpr -o area.xvg -tv volume.xvg



However, looking at the area.xvg with xmgrace, I can only see the hydrophobic 
area not the hydrophilic. Besides, looking at the volume.xvg I can only see the 
volume, not the density. Could anyone help me to see both hydrophobic and 
hydrophilic area of my protein as well as its volume and density?





Any help will highly been appreciated.



Best,

C.
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Re: [gmx-users] Colchicine topology

[Alex]

That's not my intention - someone seeking a topology would do well to a)
know the past research to inform their decisions, including whether to
repeat deliberately, and b) also ask them to share input files.

I was obviously joking, not to derail this thread. Besides, in 
biomolecular fields, FF development in general and topology building in 
particular, you guys have at least some unity in how to approach things. 
In solid state (or solid-liquid systems), we have a pretty arbitrary 
zoo. The cherry on top of this cake is recent OPLS-AA-based FF for two 
widely studied nanomaterials with partial charges coming from DDAP, 
which is entirely different from CHELPG used for OPLS originally. And 
everything fits everything!

A lot of past work is horrible, yes :-)


Always!

Alex


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Re: [gmx-users] Colchicine topology

[Mark Abraham]

Hi,

On Mon, May 28, 2018 at 9:17 AM Alex  wrote:

> Mark, please don't be one of those people telling young researchers that
> everything has already been done. :)
>

That's not my intention - someone seeking a topology would do well to a)
know the past research to inform their decisions, including whether to
repeat deliberately, and b) also ask them to share input files.


> My postdoc (a fellow, actually -- with her own project & funding) is
> reading all these horrible papers and, according to her, everything has
> been done. Drives me nuts!
>

A lot of past work is horrible, yes :-)

Mark


> Alex
>
>
> On 5/28/2018 1:11 AM, Mark Abraham wrote:
> > Hi,
> >
> > I found a couple of papers doing MD on colchicine and tubulin in a few
> > minutes on Google - maybe you should start there and also check your work
> > will be novel :-)
> >
> > Mark
> >
> > On Sat, May 26, 2018 at 8:00 AM Harutyun Sahakyan 
> > wrote:
> >
> >> Hi all,
> >>
> >>
> >>
> >> I use gromacs for MD simulations, but use charmm or amber force fields,
> did
> >> someone try to generate the colchicine topology? I try to do it using
> >> CGenFF, but get to high penalty score due to dihedrals. And which force
> >> field is better for protein-ligand simulation (tubulin-colchicine)?
> >>
> >>
> >>
> >> Thank you in advance,
> >>
> >> Harut
> >> --
> >> Gromacs Users mailing list
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> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
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> >>
>
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Re: [gmx-users] Colchicine topology

[Alex]

Mark, please don't be one of those people telling young researchers that 
everything has already been done. :)


My postdoc (a fellow, actually -- with her own project & funding) is 
reading all these horrible papers and, according to her, everything has 
been done. Drives me nuts!


Alex


On 5/28/2018 1:11 AM, Mark Abraham wrote:

Hi,

I found a couple of papers doing MD on colchicine and tubulin in a few
minutes on Google - maybe you should start there and also check your work
will be novel :-)

Mark

On Sat, May 26, 2018 at 8:00 AM Harutyun Sahakyan 
wrote:


Hi all,



I use gromacs for MD simulations, but use charmm or amber force fields, did
someone try to generate the colchicine topology? I try to do it using
CGenFF, but get to high penalty score due to dihedrals. And which force
field is better for protein-ligand simulation (tubulin-colchicine)?



Thank you in advance,

Harut
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Re: [gmx-users] Colchicine topology

[Mark Abraham]

Hi,

I found a couple of papers doing MD on colchicine and tubulin in a few
minutes on Google - maybe you should start there and also check your work
will be novel :-)

Mark

On Sat, May 26, 2018 at 8:00 AM Harutyun Sahakyan 
wrote:

> Hi all,
>
>
>
> I use gromacs for MD simulations, but use charmm or amber force fields, did
> someone try to generate the colchicine topology? I try to do it using
> CGenFF, but get to high penalty score due to dihedrals. And which force
> field is better for protein-ligand simulation (tubulin-colchicine)?
>
>
>
> Thank you in advance,
>
> Harut
> --
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Re: [gmx-users] Solvation of the bilayer

[Alex]

What are the dimensions of your bilayer and your box, and where do the 
water molecules go?



On 5/28/2018 12:20 AM, Amali Guruge wrote:

Dear Gromacs users,

I have a bilayer in xy plane. I tried to solvate the bilayer
(sur_bilayer.pdb) with water molecules using gmx solvate. I used the
command;
gmx solvate -cp sur_bilayer.pdb -maxsol 28197 -o sur_water_bilayer.pdb

However, water molecules are not distributed in the hydrophilic layers in
the xy plane as I wanted. How can I solve this problem?


Thank you.






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[gmx-users] Solvation of the bilayer

[Amali Guruge]

Dear Gromacs users,

I have a bilayer in xy plane. I tried to solvate the bilayer
(sur_bilayer.pdb) with water molecules using gmx solvate. I used the
command;
gmx solvate -cp sur_bilayer.pdb -maxsol 28197 -o sur_water_bilayer.pdb

However, water molecules are not distributed in the hydrophilic layers in
the xy plane as I wanted. How can I solve this problem?


Thank you.




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