Re: [gmx-users] Gromacs tutorial

[Nidhi singh]

The file is not recognising your .str file. The name must be different in
your mol2 file and str file. You just need to rectify that.



On Fri, 11 Oct 2019 at 8:51 PM, Suprim Tha 
wrote:

> I was trying gromacs tutorial on molecular dynamics simulation of
> protein-ligand complex. Everything was going well until the step to
> convert CHARMM
> jz4.str file into GROMACS files using the command
> python cgenff_charmm2gmx_py2.py JZ4 jz4.mol2 jz4.str charmm36-mar2019.ff
> The error was:
> Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (22) and
> top (0) are unequal
> Usually this means the specified residue name does not match between str
> and mol2 files.
> I have attached the generated str and mol2 files.
> Please help me find the error.
> --
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-- 
Dr. Nidhi
PhD
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[gmx-users] Generation of force field for "NME " capping group

[nidhi]

Dear Gromacs users,

I want to capped the end groups of a protein chain with acetyl  (ACE) and
amine  (NME) groups. As I am using gromos96 43A1 force field and NMe is not
present in aminoacid.rtp.
In amber NME is present but not in gromos.

Anyone please suggest something how to generate force field for "Nme" in
gromos.

Regards
Nidhi
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[gmx-users] Query regarding capping group "NME"

[nidhi]

Dear Gromacs users,

I want to capped the end groups of a protein chain with acetyl  (ACE) and
amine  (NME) groups. As I am using gromos96 43A1 force field and NMe is not
present in aminoacid.rtp.
In amber NME is present but not in gromos.

Anyone please suggest something how to generate force field for "Nme" in
gromos.

Regards
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Re: [gmx-users] Doubt in nmol tool

[nidhi]

Dhanyavad!!

On Mon, 8 Apr 2019, 16:34 Soham Sarkar,  wrote:

> No need to use -nmol
>
> On Mon, 8 Apr 2019, 4:21 pm nidhi,  wrote:
>
> > That means there is no need of using -nmol option.
> >
> > Thank You very much :)
> >
> >
> > On Mon, Apr 8, 2019 at 3:57 PM Soham Sarkar  wrote:
> >
> > > In that case select all c-alpha and make a group in index.ndx and run
> gmx
> > > gyrate for this group only and you are done.
> > >
> > > On Mon, 8 Apr 2019, 3:09 pm nidhi,  wrote:
> > >
> > > > I want to to calculate Rg of whole protein in the simulation box at a
> > > time
> > > > not the individual chains.
> > > > And for this I have selected Rg for "C-alpha" atoms plus  "-nmol 3" .
> > > >
> > > > Thank You,
> > > > Sundari
> > > >
> > > > On Mon, Apr 8, 2019 at 2:50 PM Soham Sarkar 
> > wrote:
> > > >
> > > > > What do you want?
> > > > > Do you want to calculate the radius of gyration of the three chain
> > at a
> > > > > time?
> > > > > If so then make a index of these protein chains together and
> > calculate
> > > rg
> > > > > by selecting it. If not then calculate the chain's rg individually.
> > > > > -Soham
> > > > >
> > > > > On Mon, 8 Apr 2019, 2:36 pm Sundari,  wrote:
> > > > >
> > > > > > Dear Gromacs users,
> > > > > >
> > > > > > Can anyone explain about -nmol (number of molecules ) option in
> gmx
> > > > > gyrate
> > > > > > tool. According to me I have 3 peptide chains in my simulation
> box
> > > and
> > > > I
> > > > > am
> > > > > > using " -nmol  3".
> > > > > > Is it correct what I have used for this option?
> > > > > >
> > > > > > Regards
> > > > > > Sundari
> > > > > > --
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> before
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Re: [gmx-users] Doubt in nmol tool

[nidhi]

That means there is no need of using -nmol option.

Thank You very much :)


On Mon, Apr 8, 2019 at 3:57 PM Soham Sarkar  wrote:

> In that case select all c-alpha and make a group in index.ndx and run gmx
> gyrate for this group only and you are done.
>
> On Mon, 8 Apr 2019, 3:09 pm nidhi,  wrote:
>
> > I want to to calculate Rg of whole protein in the simulation box at a
> time
> > not the individual chains.
> > And for this I have selected Rg for "C-alpha" atoms plus  "-nmol 3" .
> >
> > Thank You,
> > Sundari
> >
> > On Mon, Apr 8, 2019 at 2:50 PM Soham Sarkar  wrote:
> >
> > > What do you want?
> > > Do you want to calculate the radius of gyration of the three chain at a
> > > time?
> > > If so then make a index of these protein chains together and calculate
> rg
> > > by selecting it. If not then calculate the chain's rg individually.
> > > -Soham
> > >
> > > On Mon, 8 Apr 2019, 2:36 pm Sundari,  wrote:
> > >
> > > > Dear Gromacs users,
> > > >
> > > > Can anyone explain about -nmol (number of molecules ) option in gmx
> > > gyrate
> > > > tool. According to me I have 3 peptide chains in my simulation box
> and
> > I
> > > am
> > > > using " -nmol  3".
> > > > Is it correct what I have used for this option?
> > > >
> > > > Regards
> > > > Sundari
> > > > --
> > > > 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
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> > > >
> > > --
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> > >
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Re: [gmx-users] Doubt in nmol tool

[nidhi]

I want to to calculate Rg of whole protein in the simulation box at a time
not the individual chains.
And for this I have selected Rg for "C-alpha" atoms plus  "-nmol 3" .

Thank You,
Sundari

On Mon, Apr 8, 2019 at 2:50 PM Soham Sarkar  wrote:

> What do you want?
> Do you want to calculate the radius of gyration of the three chain at a
> time?
> If so then make a index of these protein chains together and calculate rg
> by selecting it. If not then calculate the chain's rg individually.
> -Soham
>
> On Mon, 8 Apr 2019, 2:36 pm Sundari,  wrote:
>
> > Dear Gromacs users,
> >
> > Can anyone explain about -nmol (number of molecules ) option in gmx
> gyrate
> > tool. According to me I have 3 peptide chains in my simulation box and I
> am
> > using " -nmol  3".
> > Is it correct what I have used for this option?
> >
> > Regards
> > Sundari
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Secondary structure content

[nidhi]

I also have same doubt.

On 9 Sep 2017 11:13 p.m., "nidhi" <nidhi020...@gmail.com> wrote:

> Thank you :)
> Can you please suggest me than what's the last line of scount.xvg file
> indicates?
> It is ss(%), what does it mean? Which kind of  secondary structure
> percentage is this?
>
> Thank you for your time and help..
>
> On 9 Sep 2017 7:03 p.m., "Justin Lemkul" <jalem...@vt.edu> wrote:
>
>>
>>
>> On 9/9/17 9:30 AM, Smith, Micholas D. wrote:
>>
>>> If i remember correctly the DSSP plot should be something like residue #
>>> on y-axis, and time on the x-axis, then it is normally a color plot of what
>>> secondary structure each residue is in at that time point. Secondary
>>> structure content (%) vs time sounds more like a single plot of the
>>> fraction of residues (%) of residues at each time point that are not in a
>>> 'coil' state.
>>>
>>>
>> That's just the ss.xpm file.  The scount.xvg has a time series of the
>> number of residues in each type of secondary structure over time.  To the
>> OP's question, it is not a percentage, it is the number of residues, from
>> which computing percentage is trivial based on the number of total residues.
>>
>> -Justin
>>
>> Hope that makes sense.
>>> ===
>>> Micholas Dean Smith, PhD.
>>> Post-doctoral Research Associate
>>> University of Tennessee/Oak Ridge National Laboratory
>>> Center for Molecular Biophysics
>>>
>>> 
>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sundari
>>> <sundi6...@gmail.com>
>>> Sent: Saturday, September 09, 2017 5:48 AM
>>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>>> Subject: [gmx-users] Secondary structure content
>>>
>>> Dear all,
>>> I am confused with 'dssp' output graph i.e "number of residues vs time".
>>> Is
>>> it also called "secondary structure content(%) vs time" ?? Or it is
>>> different term?
>>>
>>> please, anyone help me to solve this confusion  or send me any link
>>> contained proper definition of these two.
>>>
>>> Thanks in advance
>>> --
>>> 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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>>> 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
>>
>> ==
>> --
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>>
>
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Re: [gmx-users] Secondary structure content

[nidhi]

Thank you :)
Can you please suggest me than what's the last line of scount.xvg file
indicates?
It is ss(%), what does it mean? Which kind of  secondary structure
percentage is this?

Thank you for your time and help..

On 9 Sep 2017 7:03 p.m., "Justin Lemkul"  wrote:

>
>
> On 9/9/17 9:30 AM, Smith, Micholas D. wrote:
>
>> If i remember correctly the DSSP plot should be something like residue #
>> on y-axis, and time on the x-axis, then it is normally a color plot of what
>> secondary structure each residue is in at that time point. Secondary
>> structure content (%) vs time sounds more like a single plot of the
>> fraction of residues (%) of residues at each time point that are not in a
>> 'coil' state.
>>
>>
> That's just the ss.xpm file.  The scount.xvg has a time series of the
> number of residues in each type of secondary structure over time.  To the
> OP's question, it is not a percentage, it is the number of residues, from
> which computing percentage is trivial based on the number of total residues.
>
> -Justin
>
> Hope that makes sense.
>> ===
>> Micholas Dean Smith, PhD.
>> Post-doctoral Research Associate
>> University of Tennessee/Oak Ridge National Laboratory
>> Center for Molecular Biophysics
>>
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sundari <
>> sundi6...@gmail.com>
>> Sent: Saturday, September 09, 2017 5:48 AM
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: [gmx-users] Secondary structure content
>>
>> Dear all,
>> I am confused with 'dssp' output graph i.e "number of residues vs time".
>> Is
>> it also called "secondary structure content(%) vs time" ?? Or it is
>> different term?
>>
>> please, anyone help me to solve this confusion  or send me any link
>> contained proper definition of these two.
>>
>> Thanks in advance
>> --
>> 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.
>>
>>
> --
> ==
>
> 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] Calculation of nematic order parameter using gromacs

[nidhi sorout]

Thank you all..
I am a newly research scholar that's why taking some time in understanding
:)
I will try again..

Nidhi

On 3 Jun 2017 7:49 p.m., "André Farias de Moura" <mo...@ufscar.br> wrote:

> Nidhi,
>
> you need some background reading on the specifics of your problem/system
> (including order parameters for liquid crystals and other orderly systems)
> before you can do a meaningful modeling and that is up to you (it is your
> research problem, not ours)
>
> as I told you, the director makes sense only when you define that there is
> some sort of anisotropy in your system, either raised by an external field
> or by an interface. If you don't have any fields or interfaces (e.g. a free
> protein tumbling in an aqueous solution) then any direction is equally
> probable and a long enough simulation would average out to zero any order
> parameter with respect to any arbitrarily chosen director (which is one of
> the ways you may define what an isotropic solution is)
>
> Andre
>
> On Sat, Jun 3, 2017 at 3:09 AM, nidhi sorout <nidhi020...@gmail.com>
> wrote:
>
> > In my case for second  order parameter I need the angle between the unit
> > vector linking N- and C-termini of the ith peptide and the  d (the
> > director) is a unit vector defining the preferred direction of alignment.
> >
> > These vectors are not clear to me.. please suggest something.
> >
> >
> > Nidhi
> >
> > On Sat, Jun 3, 2017 at 5:10 AM, André Farias de Moura <mo...@ufscar.br>
> > wrote:
> >
> > > Hi Nidhi,
> > >
> > > In short: you are using a general-purpose software, so it does not have
> > > tools for all specific applications any user might be interested in.
> > Either
> > > you have to hack/adapt existing analysis tools or you have to write
> your
> > > own tools.
> > >
> > > That being said: the director is a rather arbitrary direction even
> > > experimentally, it becomes well-defined only when you have an external
> > > field (usually magnetic or electric, maybe both) or an interface, so
> the
> > > director would be either the direction of the field or the direction
> > > perpendicular to the interface, respectively.
> > >
> > > Anyway, it is up to you to decide which direction makes sense as the
> > > director of your system. Once you choose that vector and a vector
> > defining
> > > what you are naming "molecular axis", calculating angles and
> correlation
> > > functions to obtain any sort of order parameter can be accomplished
> > > straightforwardly using any spreadsheet.
> > >
> > > (pretty much the same Antonio had already told you)
> > >
> > > Andre
> > >
> > > On Fri, Jun 2, 2017 at 6:21 PM, nidhi sorout <nidhi020...@gmail.com>
> > > wrote:
> > >
> > > > Hello,
> > > >
> > > > Thank you Antonio..
> > > >
> > > > But my angle of interest is the angle between the molecular axis of
> > > protein
> > > > and the director. I am not able to understand here, from where I can
> > > choose
> > > > this 'director'?
> > > >
> > > > Nidhi
> > > >
> > > > On 30 May 2017 8:55 p.m., "Antonio Baptista" <bapti...@itqb.unl.pt>
> > > wrote:
> > > >
> > > > > Hi Nidhi,
> > > > >
> > > > > If I remember correctly (and your use of "p2" suggests so), that
> > should
> > > > be
> > > > > the ensemble average of the 2nd-order Legendre polynomial of the
> > angle
> > > > > between the molecular axis and the membrane normal, right?
> > > > >
> > > > > Although the order parameter computed by "gmx order" uses that same
> > > > > definition, it takes each C-H bond of the aliphatic lipid tail, not
> > the
> > > > > overall molecular axis. So, "gmx order" is not what you want.
> > > > >
> > > > > You can in principle compute what you need in two steps: (1) use
> "gmx
> > > > > gangle" to compute the angle of interest for all molecules and all
> > > > > snapshots (you will have to defined the vector of interest, say as
> > the
> > > > one
> > > > > connecting the tail to the head); (2) do a small script to compute
> > the
> > > > > average from those data.
> > > > >
> > > > > Best,
> > >

Re: [gmx-users] Calculation of nematic order parameter using gromacs

[nidhi sorout]

In my case for second  order parameter I need the angle between the unit
vector linking N- and C-termini of the ith peptide and the  d (the
director) is a unit vector defining the preferred direction of alignment.

These vectors are not clear to me.. please suggest something.


Nidhi

On Sat, Jun 3, 2017 at 5:10 AM, André Farias de Moura <mo...@ufscar.br>
wrote:

> Hi Nidhi,
>
> In short: you are using a general-purpose software, so it does not have
> tools for all specific applications any user might be interested in. Either
> you have to hack/adapt existing analysis tools or you have to write your
> own tools.
>
> That being said: the director is a rather arbitrary direction even
> experimentally, it becomes well-defined only when you have an external
> field (usually magnetic or electric, maybe both) or an interface, so the
> director would be either the direction of the field or the direction
> perpendicular to the interface, respectively.
>
> Anyway, it is up to you to decide which direction makes sense as the
> director of your system. Once you choose that vector and a vector defining
> what you are naming "molecular axis", calculating angles and correlation
> functions to obtain any sort of order parameter can be accomplished
> straightforwardly using any spreadsheet.
>
> (pretty much the same Antonio had already told you)
>
> Andre
>
> On Fri, Jun 2, 2017 at 6:21 PM, nidhi sorout <nidhi020...@gmail.com>
> wrote:
>
> > Hello,
> >
> > Thank you Antonio..
> >
> > But my angle of interest is the angle between the molecular axis of
> protein
> > and the director. I am not able to understand here, from where I can
> choose
> > this 'director'?
> >
> > Nidhi
> >
> > On 30 May 2017 8:55 p.m., "Antonio Baptista" <bapti...@itqb.unl.pt>
> wrote:
> >
> > > Hi Nidhi,
> > >
> > > If I remember correctly (and your use of "p2" suggests so), that should
> > be
> > > the ensemble average of the 2nd-order Legendre polynomial of the angle
> > > between the molecular axis and the membrane normal, right?
> > >
> > > Although the order parameter computed by "gmx order" uses that same
> > > definition, it takes each C-H bond of the aliphatic lipid tail, not the
> > > overall molecular axis. So, "gmx order" is not what you want.
> > >
> > > You can in principle compute what you need in two steps: (1) use "gmx
> > > gangle" to compute the angle of interest for all molecules and all
> > > snapshots (you will have to defined the vector of interest, say as the
> > one
> > > connecting the tail to the head); (2) do a small script to compute the
> > > average from those data.
> > >
> > > Best,
> > > Antonio
> > >
> > >
> > > On Tue, 30 May 2017, nidhi sorout wrote:
> > >
> > > Dear All,
> > >> I want to calculate the nematic order parameter (p2) at each time
> step.
> > >> Is it possible to do this with "gmx order"?
> > >> If not than  please suggest the right way.
> > >>
> > >> Thank you,
> > >> Nidhi
> > >> --
> > >> 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!
> > >
> > > * 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!
> >
> > * 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-us

Re: [gmx-users] Calculation of nematic order parameter using gromacs

[nidhi sorout]

Hello,

Thank you Antonio..

But my angle of interest is the angle between the molecular axis of protein
and the director. I am not able to understand here, from where I can choose
this 'director'?

Nidhi

On 30 May 2017 8:55 p.m., "Antonio Baptista" <bapti...@itqb.unl.pt> wrote:

> Hi Nidhi,
>
> If I remember correctly (and your use of "p2" suggests so), that should be
> the ensemble average of the 2nd-order Legendre polynomial of the angle
> between the molecular axis and the membrane normal, right?
>
> Although the order parameter computed by "gmx order" uses that same
> definition, it takes each C-H bond of the aliphatic lipid tail, not the
> overall molecular axis. So, "gmx order" is not what you want.
>
> You can in principle compute what you need in two steps: (1) use "gmx
> gangle" to compute the angle of interest for all molecules and all
> snapshots (you will have to defined the vector of interest, say as the one
> connecting the tail to the head); (2) do a small script to compute the
> average from those data.
>
> Best,
> Antonio
>
>
> On Tue, 30 May 2017, nidhi sorout wrote:
>
> Dear All,
>> I want to calculate the nematic order parameter (p2) at each time step.
>> Is it possible to do this with "gmx order"?
>> If not than  please suggest the right way.
>>
>> Thank you,
>> Nidhi
>> --
>> 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!
>
> * 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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[gmx-users] Calculation of nematic order parameter using gromacs

[nidhi sorout]

Dear All,
 I want to calculate the nematic order parameter (p2) at each time step.
Is it possible to do this with "gmx order"?
If not than  please suggest the right way.

Thank you,
Nidhi
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[gmx-users] problem in parametrization of NH2 group

[Nidhi Batra]

Dear All
I want to run a simulation for a protein-peptide complex where the N- 
C-terminal of the peptide is capped by acetyl and amine (NH2) group
respectively. I am using the charmm36ff but couldn't find the parameters
for NH2 group anywhere. I tried using SwissParam to generate the .itp but
don't know how to convert it to .rtp.

Kindly help regarding this.



Thanking you

Yours sincerely
-- 
Nidhi Batra
DBT-Research Associate
Institute of Genomics and Integrative Biology (IGIB),
Mathura Road, Sukhdev Vihar
New Delhi 110020
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[gmx-users] mean square displacement

[Nidhi Katyal]

Hello all

I would like to plot mean square displacement of hydrogen atoms of protein
versus temperature (in order to get dynamical transition temperature). I am
using g_msd for this purpose (g_msd -f *_nopbc.xtc -s *.tpr -n index.ndx -o
*.xvg) . I am getting following curves as uploded in :

http://s903.photobucket.com/user/nidhikatyal1989/media/msd_fig1_zpsc293a5ab.jpg.html


How should I plot msd value versus temperature? Is it reasonable enough to
take average over 2 ns (linear part) and discard the rest? Moreover, I
suspect there is something wrong in the curves too since they are
increasing first, reaching saturation and again increasing (last part is
unexpected).

Actually I am trying to reproduce the results of following paper:
 THE JOURNAL OF CHEMICAL PHYSICS 130, 135101 
2009, FIG 9 (a)

My values are also deviating by larger amount. Am I doing something wrong?

Please help.

Thanks
Nidhi
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Re: [gmx-users] regarding MSD

[Nidhi Katyal]

Please reply.

Reposting the same query again:

I have read few papers that determine transition temperature from the plot
of average MSD of hydrogen atoms of protein versus temperature. My question
is:
At a particular temperature, we get a linear curve for MSD versus time, is
it reasonable to calculate average MSD over all such time points? Is this
the average that is plotted in papers (or something is missing) ? My doubt
is won't this average depend on the number of time points (due to its
linear nature)?

Actually I am trying to reproduce the results of some published data.
Although I am getting the same transition temperature but the MSD values
are coming different (eg at a particular temperature if I average all the
MSD values, I am getting value of 15000 while reported value is 1.5 - both
values in same unit angstrom square)




On Fri, Aug 22, 2014 at 7:15 PM, Nidhi Katyal nidhikatyal1...@gmail.com
wrote:



 -- Forwarded message --
 From: Nidhi Katyal nidhikatyal1...@gmail.com
 Date: Fri, Aug 22, 2014 at 11:41 AM
 Subject: Re: regarding MSD
 To: Discussion list for GROMACS users gmx-us...@gromacs.org


 Hello

 I have posted the query earlier but havent got any reply and so reposting
 it again.

 I have read few papers that determine transition temperature from the plot
 of average MSD of hydrogen atoms of protein versus temperature. My question
 is:
 At a particular temperature, we get a linear curve for MSD versus time, is
 it reasonable to calculate average MSD over all such time points? Is this
 the average that is plotted in papers (or something is missing) ? My doubt
 is won't this average depend on the number of time points (due to its
 linear nature)?

 Actually I am trying to reproduce the results of some published data.
 Although I am getting the same transition temperature but the MSD values
 are coming different (eg at a particular temperature if I average all the
 MSD values, I am getting value of 15000 while reported value is 1.5 - both
 values in same unit angstrom square)

 Any help is highly appreciated.



 On Thu, Aug 21, 2014 at 9:56 PM, Nidhi Katyal nidhikatyal1...@gmail.com
 wrote:

 Hello all

 I have read few papers that determine transition temperature from the
 plot of average MSD versus temperature. My question is:
 At a particular temperature, we get a linear curve for MSD versus time,
 is it reasonable to calculate average MSD over all such time points? Is
 this the average that is plotted in papers (or something is missing) ? My
 doubt is won't this average depend on the number of time points (due to its
 linear nature)?
 Any help is highly appreciated.

 Thanks
 Nidhi




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Re: [gmx-users] regarding MSD

[Nidhi Katyal]

Hello

I have posted the query earlier but havent got any reply and so reposting
it again.

I have read few papers that determine transition temperature from the plot
of average MSD of hydrogen atoms of protein versus temperature. My question
is:
At a particular temperature, we get a linear curve for MSD versus time, is
it reasonable to calculate average MSD over all such time points? Is this
the average that is plotted in papers (or something is missing) ? My doubt
is won't this average depend on the number of time points (due to its
linear nature)?

Actually I am trying to reproduce the results of some published data.
Although I am getting the same transition temperature but the MSD values
are coming different (eg at a particular temperature if I average all the
MSD values, I am getting value of 15000 while reported value is 1.5 - both
values in same unit angstrom square)

Any help is highly appreciated.



On Thu, Aug 21, 2014 at 9:56 PM, Nidhi Katyal nidhikatyal1...@gmail.com
wrote:

 Hello all

 I have read few papers that determine transition temperature from the plot
 of average MSD versus temperature. My question is:
 At a particular temperature, we get a linear curve for MSD versus time, is
 it reasonable to calculate average MSD over all such time points? Is this
 the average that is plotted in papers (or something is missing) ? My doubt
 is won't this average depend on the number of time points (due to its
 linear nature)?
 Any help is highly appreciated.

 Thanks
 Nidhi

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[gmx-users] regarding g_hydorder

[Nidhi Katyal]

Hello all

I would like to calculate both distance and angle water orientational
order. I have made an index file containing all oxygen atoms of water and
used trjorder as:
g_hydorder -f *.xtc -s *.tpr -n *.ndx -o file1_1 file2_1 -or file1_2 file2_2
How to interpret the results of the output files? Both output files file1_2
and file2_2 contain the same content. Won't one should contain distance and
other angle orientational order parameter values?
Also I expect parameter values to be less than or equal to 1. But the
values in the file looks something like the following (all greater than 1):

 #Legend   #TBlock   #Xbin Ybin Z t  0   0 0 6.5  0 1 6.5  0 2 4.5  0 3 3.5
0 4 6.5  0 5 4.5  0 6 5.5  1 0 6.5  1 1 4.5  1 2 5.5  1 3 3.5  1 4 5.5  1 5
4.5  1 6 5.5  2 0 4.5  .
.


  Please help me in interpreting this file.

Thanks
Nidhi
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[gmx-users] regarding MSD

[Nidhi Katyal]

Hello all

I have read few papers that determine transition temperature from the plot
of average MSD versus temperature. My question is:
At a particular temperature, we get a linear curve for MSD versus time, is
it reasonable to calculate average MSD over all such time points? Is this
the average that is plotted in papers (or something is missing) ? My doubt
is won't this average depend on the number of time points (due to its
linear nature)?
Any help is highly appreciated.

Thanks
Nidhi
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Re: [gmx-users] atoms are not part of any of the T-Coupling groups

[Nidhi Katyal]

gmxcheck of my index file gives:

Contents of index file index.ndx
--
Nr.   Group   #Entries   FirstLast
   0  System  2230   12230
   1  Protein 2226   12226
   2  Protein-H   2226   12226
   3  C-alpha  308   32218
   4  Backbone 922   12219
   5  MainChain   1232   12226
   6  MainChain+Cb1488   12226
   7  MainChain+H 1232   12226
   8  SideChain994   82225
   9  SideChain-H  994   82225
  10  Prot-Masses 2226   12226
  11  non-Protein422272230
  12  Ion422272230
  13  CU 222272229
  14  ZN 222282230
  15  r_131__chA8 956 963
  16  r_131__chB820692076
  17  r_132 1112071217
  18  r_286 1126112621
  19  CA_chA_r131112091209
  20  CA_chB_r131126132613

and following are the contents of my .mdp file:

title   = Umbrella pulling simulation
define  = -DPOSRES_CA_chA_r131
; 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  Non-Protein
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= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= Y N N
pull_start  = yes   ; define initial COM distance  0
pull_ngroups= 1
pull_group0 = CA_chA_r131
pull_group1 = CA_chB_r131
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 4200  ; kJ mol^-1 nm^-2

Thanks in advance.

Nidhi




On Wed, Aug 6, 2014 at 8:06 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 8/6/14, 3:46 AM, Nidhi Katyal wrote:

 Hello all,

 I am working on protein with two chains. I would like to restrain one atom
 of one chain while doing steered MD. For the same reason, I have created
 an
 index file that includes that atom, then created its posre.itp file and
 finally included following lines at the end of topol_Protein_chainA.itp:

 ; Include Position restraint file
 #ifdef POSRES_CA_chA_r131
 #include posre.itp
 #endif

 I am also pasting a small section of my topol.top file:


 ; Include forcefield parameters
 #include gromos53a6.ff/forcefield.itp

 ; Include chain topologies
 #include topol_Protein_chain_A.itp
 #include topol_Protein_chain_B.itp
 #include topol_Ion_chain_A2.itp
 #include topol_Ion_chain_B2.itp

 ; Include water topology
 #include gromos53a6.ff/spc.itp

 #ifdef POSRES_WATER
 ; Position restraint for each water oxygen
 [ position_restraints ]
 ;  i funct   fcxfcyfcz
 11   1000   1000   1000
 #endif

 After carrying out NPT equilibration, when I run following command:

 grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt
 -o pull.tpr

 as given in tutorial:
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
 gmx-tutorials/umbrella/05_pull.html

 I am getting following error:
 215400 atoms are not part of any of the T-Coupling groups

 Since my pull.mdp file as the same as given in tutorial, my coupling
 groups are Protein and Non-Protein.
 I suspect there is something wrong while adding restraints using
 include file mechanism. Please help me resolve the problem.


 The error is not a result of the #include mechanism; it's a problem in the
 group definitions, either in the .mdp file or in the index file.  Without
 the full text of the .mdp and the gmxcheck output of the index.ndx file,
 there's little to suggest.

 -Justin

[gmx-users] atoms are not part of any of the T-Coupling groups

[Nidhi Katyal]

Hello all,

I am working on protein with two chains. I would like to restrain one atom
of one chain while doing steered MD. For the same reason, I have created an
index file that includes that atom, then created its posre.itp file and
finally included following lines at the end of topol_Protein_chainA.itp:

; Include Position restraint file
#ifdef POSRES_CA_chA_r131
#include posre.itp
#endif

I am also pasting a small section of my topol.top file:


; Include forcefield parameters
#include gromos53a6.ff/forcefield.itp

; Include chain topologies
#include topol_Protein_chain_A.itp
#include topol_Protein_chain_B.itp
#include topol_Ion_chain_A2.itp
#include topol_Ion_chain_B2.itp

; Include water topology
#include gromos53a6.ff/spc.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

After carrying out NPT equilibration, when I run following command:

grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt
-o pull.tpr

as given in tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html

I am getting following error:
215400 atoms are not part of any of the T-Coupling groups

Since my pull.mdp file as the same as given in tutorial, my coupling
groups are Protein and Non-Protein.
I suspect there is something wrong while adding restraints using
include file mechanism. Please help me resolve the problem.

Thanks
Nidhi
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Re: [gmx-users] Groups in index.ndx

[Nidhi Katyal]

Use make_ndx -f *.gro -n old_index.ndx -o old_index.ndx


On Fri, Jul 25, 2014 at 4:53 PM, INPE (Ingrid Viveka Pettersson) 
i...@novonordisk.com wrote:

 Dear Group,

 I have defined different specific groups in the index.ndx file. My problem
 is that if I try to add a new group, the old ones are disappearing. Should
 it be like this?

 Yours sincerely,

 Ingrid Pettersson


 _

 Ingrid Pettersson, PhD
 Principal Scientist
 Diabetes Structural Biology

 Novo Nordisk A/S
 Novo Nordisk Park
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 Denmark
 +4530754506 (direct)
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[gmx-users] Running job on GPUs

[Nidhi Katyal]

Hello all

I am trying to run my job on 2 nodes by utilizing all available cores. On
each node of the cluster, we have two GPUs and two sockets with 8 cores
each.
Every time I am submitting the job, we find that it is running on one node.
How to make use of the other node?

Till now, I have used following trial commands as suggested in
http://www.gromacs.org/Documentation/Acceleration_and_parallelization

1)  mpirun -n 2 mdrun_mpi -v -deffnm nvt -ntomp 16

output:

Using 2 MPI processes
Using 16 OpenMP threads per MPI process

WARNING: Oversubscribing the available 16 logical CPU cores with 32 threads.
 This will cause considerable performance loss!

2)  mpirun -n 4 mdrun_mpi -v -deffnm nvt -ntomp 8

output:

Incorrect launch configuration: mismatching number of PP MPI processes and
GPUs per node.
mdrun_mpi was started with 4 PP MPI processes per node, but only 2 GPUs
were detected.

I understand that the above error comes when number of MPI ranks is not a
multiple of number of GPUs intended to be used. But in my case 4 is a
multiple of 2.

3) mpirun -n 4 -npernode 2 mdrun_mpi -v -deffnm nvt

The job still runs on 1 node.

How can I run my job on 2 nodes utilizing all cores and GPUs?

Thanks
Nidhi
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[gmx-users] g_hbond

[Nidhi Katyal]

Hi all,

I have created hydrogen bond existence map. In the index file generated
using hbn option I can see following lines at the end:
   1  2   1598
  1  2   1851
  1  2   1852
  1  2   1862
 10 11   1643
 10 11   1651
 10 11   1658
 10 11   1664
 10 11   1682
 10 11   1748
 10 11   1754
 10 11   1761
 10 11   1762
 10 11   1772
 10 11   1830
 10 11   1831
 10 11   1838
 10 11   1851
 10 11   1862

There are 19 lines in total and also in the existence map created using hbm
option, I could see 19 lines. But when I generate index file with a2 and
calculate hydrogen bond with my ligand moleules, I can see zero bonds. Am I
doing something wrong?

Thanks
Nidhi
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[gmx-users] Hydrogen bond existence map

[Nidhi Katyal]

Hi all

I would like to create hydrogen bond existence map for interaction of each
residue with my ligand. I am aware that -hbm and -hbn option of g_hbond
along with index file would serve the purpose. But the resulting output
file is giving existence map for each atom of the residue. Instead, I want
one map for residue as a whole. Example if any residue of protein is
forming hydrogen bond with my ligand for certain time through bond A but
for the remaining time it forms through bond B, then I want the map to show
presence of hydrogen bond through one single line during the entire course
of simulation. Is it possible with gromacs?

Thanks in advance
Nidhi
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[gmx-users] binding sites with MD

[Nidhi Katyal]

Hi all,

I would like to ask if unbiased MD in nanoseconds time scale be used to
find the potential binding sites of ligand with protein?

I have simulated for 50ns, 1:14 and 1:24 protein:ligand simultaneously with
random placement of ligand initially. In the time interval between 40 to
50ns, movement of ligand molecules can be seen around certain sites only
for both the runs. Can these sites be considered as binding sites? Also,
ligand molecules are involved in both hydrophobic and hydrogen bonding
interactions with these sites.

Thanks in advance.
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Re: [gmx-users] parameters problem

[Nidhi Katyal]

Thanks Mark. Yes, my ligand.itp indeed has both [atomtypes] entry as well
as [molecule] entry. I have followed the following procedure to #include
while creating my first molecule:
Run pdb2gmx command.
Added #include ligand.itp after
#include charmm27.ff/forcefield.itp
but before
[ moleculetype ]
; Namenrexcl
Protein_chain_A 3
and added at the end:
[ molecules ]
; Compound#mols
Protein_chain_A 1
LIG 1
SOL 17063

then I have merged protein and ligand coordinates by inserting ATOM lines
from ligand.pdb to *.pdb generated after pdb2gmx command.
Then. I run editconf, genbox and finally grompp command.

After which I got following error:
Fatal error:
No such moleculetype LIG

My both *.itp and *.pdb files contains LIG.

How to rectify the error? Thanks in advance.



On Tue, Mar 11, 2014 at 1:39 AM, Mark Abraham mark.j.abra...@gmail.comwrote:

 Probably you will see that your ligand.itp has an [atomtypes] entry as well
 as a [molecule] entry, and the former cannot follow any instance of the
 latter. Such an .itp file must be #included to create the first molecule.
 You have your protein [molecule] above the #include ligand.itp at the
 moment, which would cause this problem.

 Mark


 On Mon, Mar 10, 2014 at 7:09 PM, Nidhi Katyal nidhikatyal1...@gmail.com
 wrote:

  To test swiss param parameters, I have generated *.pdb and *.itp files
 from
  it. In the genbox command, I have used -ci *.pdb -nmol 2.
  I have included *.itp in the topology as:
 
  ; Include Position restraint file
  ;#ifdef POSRES
  ;#include posre.itp
  ;#endif
 
  ;Include ligand topology
  #include ligand.itp
 
  ; Include water topology
  #include charmm27.ff/tip3p.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 charmm27.ff/ions.itp
 
  [ system ]
  ; Name
  Protein in water
 
  [ molecules ]
  ; Compound#mols
  Protein_chain_A 1
  LIG 2
  SOL 12904
 
  But after I run grompp command, I get following error:
 
  Fatal error:
  Syntax error - File ligand.itp, line 7
  Last line read:
  '[ atomtypes ] '
  Invalid order for directive atomtypes
 
  Please help me rectify the problem of the order getting violated although
  same worked for topology generated by PRODRG.
 
  Thanks in advance.
 
 
 
  On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote:
 
  
  
   On 3/10/14, 8:21 AM, Nidhi Katyal wrote:
  
   Thanks Justin. I would also like to know the reliability of parameters
   generated using swiss param.
  
  
  
   I have no personal experience with it.  My rule is to never trust
  anything
   from a black-box server without verifying it and assessing any
  information
   about penalties, deviations, etc. that it provides.
  
   -Justin
  
  
On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul jalem...@vt.edu
 wrote:
  
  
  
   On 3/10/14, 2:45 AM, Nidhi Katyal wrote:
  
Thank you Mark and Justin.
   Now, I have carried out simulations using PME electrostatics and
 using
   all other
   parameters (except gromos 96 43a1 ff used) as suggested in
   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
   gmx-tutorials/lysozyme/
  
   The protein is not loosing its structure now. But the problem is if
 I
   carry out
   simulations in the presence of experimentally known stabiliser
  generated
   using
   ProDrg (keeping all the parameters same while simulating both in the
   presence
   and absence of stabiliser), the partial loss of secondary structure
 is
   observed
   in the presence of stabilizer relative to the case in its absence at
   350K
   thereby implying simulations going against experimental observations
   (although
   slight stabilization was observed at 300K). Simulations were
 repeated
   twice with
   two different force fields.
   However if I use above em,pr,full parameters with cut-off
   electrostatics,
   although secondary structure is lost in the initial stages but I
 could
   clearly
   see the stabilization behaviour of additive in terms of secondary
   structure
   retainment till longer time. Is this observation a matter of chance-
   reliable or
   not? What could be the possible reason for not observing such
   stabilization with
   better parameters?
  
  
Cutoff electrostatics are horribly inaccurate.  The fact that you
   conveniently see what you hope to when using a plain cutoff is likely
  by
   chance.
  
   The bigger issue is the use of PRODRG parameters.  As I have said
   numerous
   times on this list, the parameters it produces are demonstrably
   inaccurate
   and require reparametrization.
  
   http://pubs.acs.org/doi/abs/10.1021/ci100335w
  
  
   -Justin
  
   --
   ==
  
   Justin A. Lemkul, Ph.D.
   Ruth L. Kirschstein NRSA

Re: [gmx-users] parameters problem

[Nidhi Katyal]

To test swiss param parameters, I have generated *.pdb and *.itp files from
it. In the genbox command, I have used -ci *.pdb -nmol 2.
I have included *.itp in the topology as:

; Include Position restraint file
;#ifdef POSRES
;#include posre.itp
;#endif

;Include ligand topology
#include ligand.itp

; Include water topology
#include charmm27.ff/tip3p.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 charmm27.ff/ions.itp

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
LIG 2
SOL 12904

But after I run grompp command, I get following error:

Fatal error:
Syntax error - File ligand.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes

Please help me rectify the problem of the order getting violated although
same worked for topology generated by PRODRG.

Thanks in advance.



On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 3/10/14, 8:21 AM, Nidhi Katyal wrote:

 Thanks Justin. I would also like to know the reliability of parameters
 generated using swiss param.



 I have no personal experience with it.  My rule is to never trust anything
 from a black-box server without verifying it and assessing any information
 about penalties, deviations, etc. that it provides.

 -Justin


  On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 3/10/14, 2:45 AM, Nidhi Katyal wrote:

  Thank you Mark and Justin.
 Now, I have carried out simulations using PME electrostatics and using
 all other
 parameters (except gromos 96 43a1 ff used) as suggested in
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
 gmx-tutorials/lysozyme/

 The protein is not loosing its structure now. But the problem is if I
 carry out
 simulations in the presence of experimentally known stabiliser generated
 using
 ProDrg (keeping all the parameters same while simulating both in the
 presence
 and absence of stabiliser), the partial loss of secondary structure is
 observed
 in the presence of stabilizer relative to the case in its absence at
 350K
 thereby implying simulations going against experimental observations
 (although
 slight stabilization was observed at 300K). Simulations were repeated
 twice with
 two different force fields.
 However if I use above em,pr,full parameters with cut-off
 electrostatics,
 although secondary structure is lost in the initial stages but I could
 clearly
 see the stabilization behaviour of additive in terms of secondary
 structure
 retainment till longer time. Is this observation a matter of chance-
 reliable or
 not? What could be the possible reason for not observing such
 stabilization with
 better parameters?


  Cutoff electrostatics are horribly inaccurate.  The fact that you
 conveniently see what you hope to when using a plain cutoff is likely by
 chance.

 The bigger issue is the use of PRODRG parameters.  As I have said
 numerous
 times on this list, the parameters it produces are demonstrably
 inaccurate
 and require reparametrization.

 http://pubs.acs.org/doi/abs/10.1021/ci100335w


 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 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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 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 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] antiparallel beta sheet

[Nidhi Katyal]

Dear users,

I would like to analyse the time variation of antiparallel beta sheet
formation. I am aware that dssp and stride program can calculate the beta
sheet content but is there a tool that can distinguish between antiparallel
and parallel beta sheet (in terms of giving numeric value as output and not
through visual inspection)?

Thanks in advance.
Nidhi
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[gmx-users] xpm2ps

[Nidhi Katyal]

Hello,

I would like to change the scale of x axis and y axis of my dssp.eps file
by different amounts. Example with xpm2ps -skip command I can write out
every nr-th row and nr-th column but I want every nr-th row and mr-th
column.
Please suggest if it is possible to do so.
Thanks in advance.

Nidhi
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[gmx-users] parameters problem

[Nidhi Katyal]

Dear all

I am trying to simulate a protein in 3 steps: energy minimization (using
em.mdp), position restraints (using pr.mdp) and final production run by NPT
ensemble (using full.mdp) at 300K

At this temperature, it is known by previous literature survey that protein
keeps its secondary structure almost intact. But according to my
simulations (done thrice), protein starts loosing its secondary structure
around 6-8ns only. I have used the following parameters:

*em.mdp*

;
; User spoel (236)
; Wed Nov  3 17:12:44 1993
; Input file
;
cpp =  /usr/bin/cpp
define  =  -DFLEX_SPC
constraints =  none
integrator  =  steep
nsteps  =  25
;
; Energy minimizing stuff
;
emtol   =  2000
emstep  =  0.001

nstcomm =  1
ns_type =  grid
rlist   =  1
rcoulomb=  1.0
rvdw=  1.0
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no


*pr.mdp*

;
; User spoel (236)
; Wed Nov  3 17:12:44 1993
; Input file
;
title   =  Yo
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints =  all-bonds
integrator  =  md
dt  =  0.002  ; ps !
nsteps  =  5  ; total 100 ps.
nstcomm =  1
nstxout =  5000
nstvout =  5000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc-grps   =  ProteinNon-protein
tau_t   =  0.10.1
ref_t   =  300300
; Energy monitoring
energygrps  =  ProteinNon-protein
; Pressure coupling is not on
Pcoupl  =  no
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529


*full.mdp*

;
; User spoel (236)
; Wed Nov  3 17:12:44 1993
; Input file
;
title   =  Yo
cpp =  /usr/bin/cpp
constraints =  all-bonds
integrator  =  md
dt  =  0.002  ; ps !
nsteps  = 2500  ; total 5 ps.
nstcomm =  1
nstxout =  5000
nstvout =  5000
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc-grps   =  Protein Non-protein
tau_t   =  0.10.1
ref_t   =  300  300
; Energy monitoring
energygrps  =  Protein  Non-protein
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
Pcoupltype  = isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is off at 300 K.
gen_vel =  no
gen_temp=  300.0
gen_seed=  173529

 I don't think it is the problem of thermostat because even after using
V-rescale for temperature coupling and Parinello Rahman for pressure
coupling, my protein loses its secondary structure in the initial time of
simulation.

Also, I have carried out various checks (like potential energy convergence
after em, temperature check after pr, and pressure and density check after
full), all of which seems to converge well.

Please help me figure out the problem.
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Re: [gmx-users] converting .xpm to .eps

[Nidhi Jatana]

I am using gromacs version 4.6.




On Fri, Dec 20, 2013 at 2:39 PM, bipin singh bipinel...@gmail.com wrote:

 Not sure, might be something going wrong due to large dimension of your
 matrix. Which Gromacs version you are using. Others may provide some clues.


 On Fri, Dec 20, 2013 at 10:04 AM, Nidhi Jatana nidhijat...@bic-svc.ac.in
 wrote:

  Dear Sir/Madam
  Please find attached the file containing the error.
 
  Thanking you
 
  Regards
  --
  Nidhi Jatana
  Senior Research Fellow
  Bioinformatics Center
  Sri Venkateswara College
  (University of Delhi)
  Dhaula Kuan
  New Delhi-110021.
 
 
 
  On Thu, Dec 19, 2013 at 7:44 PM, Carsten Kutzner ckut...@gwdg.de
 wrote:
 
   On 12/19/2013 12:53 PM, Nidhi Jatana wrote:
  
   Dear Sir/Madam
   I generated the atomic density plot using g_densmap by giving the
   following
   command:
   g_densmap -f *.xtc -s *.pdb -n *.ndx -o *.xpm
  
   The calculation completed successfully but when I am trying to convert
   .xpm
   file to .eps file using xpm2ps command, its giving error and aborts.
  
   What is the error message?
  
   If I use your set of commands with Gromacs 4.6.4, I can successfully
  create
   an EPS file.
  
   Carsten
  
  
   xpm2ps -f *.xpm -o *.eps -rainbow red -xpm *.xpm
  
   I have tried many options with setting -bx and -by but of no help. I
  also
   tried taking the .m2p file but the problem persist. Please find
 attached
   the .m2p file for reference. Please help me with this.
  
   Thanking you
  
   Regards
 --
   Nidhi Jatana
   Senior Research Fellow
   Bioinformatics Center
   Sri Venkateswara College
   (University of Delhi)
   Dhaula Kuan
   New Delhi-110021.
  
  
  
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-- 
Nidhi Jatana
Senior Research Fellow
Bioinformatics Center
Sri Venkateswara College
(University of Delhi)
Dhaula Kuan
New Delhi-110021.
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Re: [gmx-users] converting .xpm to .eps

[Nidhi Jatana]

How do you fix the matrix size? Should I do it while generation of .xpm
file or while converting it to .eps and using which option?

Regards
Nidhi


On Fri, Dec 20, 2013 at 3:35 PM, Carsten Kutzner ckut...@gwdg.de wrote:

 On 12/20/2013 10:09 AM, bipin singh wrote:

 Not sure, might be something going wrong due to large dimension of your
 matrix. Which Gromacs version you are using. Others may provide some
 clues.

 I just tried with a 483 x 486 matrix which went smoothly.
 You could try to narrow down the problem.
 See whether it works with other input data for example.
 Check whether it works on another machine.

 Carsten



 On Fri, Dec 20, 2013 at 10:04 AM, Nidhi Jatana nidhijat...@bic-svc.ac.in
 wrote:

  Dear Sir/Madam
 Please find attached the file containing the error.

 Thanking you

 Regards
 --
 Nidhi Jatana
 Senior Research Fellow
 Bioinformatics Center
 Sri Venkateswara College
 (University of Delhi)
 Dhaula Kuan
 New Delhi-110021.



 On Thu, Dec 19, 2013 at 7:44 PM, Carsten Kutzner ckut...@gwdg.de
 wrote:

  On 12/19/2013 12:53 PM, Nidhi Jatana wrote:

  Dear Sir/Madam
 I generated the atomic density plot using g_densmap by giving the
 following
 command:
 g_densmap -f *.xtc -s *.pdb -n *.ndx -o *.xpm

 The calculation completed successfully but when I am trying to convert
 .xpm
 file to .eps file using xpm2ps command, its giving error and aborts.

  What is the error message?

 If I use your set of commands with Gromacs 4.6.4, I can successfully

 create

 an EPS file.

 Carsten


  xpm2ps -f *.xpm -o *.eps -rainbow red -xpm *.xpm

 I have tried many options with setting -bx and -by but of no help. I

 also

 tried taking the .m2p file but the problem persist. Please find attached
 the .m2p file for reference. Please help me with this.

 Thanking you

 Regards
--
 Nidhi Jatana
 Senior Research Fellow
 Bioinformatics Center
 Sri Venkateswara College
 (University of Delhi)
 Dhaula Kuan
 New Delhi-110021.



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-- 
Nidhi Jatana
Senior Research Fellow
Bioinformatics Center
Sri Venkateswara College
(University of Delhi)
Dhaula Kuan
New Delhi-110021.
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[gmx-users] converting .xpm to .eps

[Nidhi Jatana]

Dear Sir/Madam
I generated the atomic density plot using g_densmap by giving the following
command:
g_densmap -f *.xtc -s *.pdb -n *.ndx -o *.xpm

The calculation completed successfully but when I am trying to convert .xpm
file to .eps file using xpm2ps command, its giving error and aborts.

xpm2ps -f *.xpm -o *.eps -rainbow red -xpm *.xpm

I have tried many options with setting -bx and -by but of no help. I also
tried taking the .m2p file but the problem persist. Please find attached
the .m2p file for reference. Please help me with this.

Thanking you

Regards
 --
Nidhi Jatana
Senior Research Fellow
Bioinformatics Center
Sri Venkateswara College
(University of Delhi)
Dhaula Kuan
New Delhi-110021.
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Gromacs Users mailing list

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