[gmx-users] md simulation for magnetic nanomaterials

2017-09-14 Thread Mohammad Zahidul Hossain Khan 
Dear Sir

I know gromacs do some md simulation for biological system. I want to do
some md simulation on magnetic nanomaterials. Can you anyone give me some
idea which software do md simulation for magnetic nanomaterials.

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*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
* Skype: parash.khan2*
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Re: [gmx-users] dielectric constant 4

2017-08-16 Thread Mohammad Zahidul Hossain Khan 
Dear sir

Thank you very much. It will help me lot

On Aug 16, 2017 8:35 PM, "Alex" <nedoma...@gmail.com> wrote:

> A meaningful answer to your question is incredibly non-trivial. Also, you
> will need a reference for your epsilon value. "Someone on gmx-users told
> me, because I don't feel like doing my own research" may not look very good
> in a manuscript.
>
> Alex
>
>
> On 8/16/2017 5:14 PM, Mohammad Zahidul Hossain Khan wrote:
>
>> Dear User
>>
>> Dose anyone know how can I use dielectric constant 4 in mdp for protein
>> during the simulation?
>>
>>
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[gmx-users] dielectric constant 4

2017-08-16 Thread Mohammad Zahidul Hossain Khan 
Dear User

Dose anyone know how can I use dielectric constant 4 in mdp for protein
during the simulation?

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*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
* Skype: parash.khan2*
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Re: [gmx-users] npt simulation error

2017-08-16 Thread Mohammad Zahidul Hossain Khan 
Dear Sir

Thank you very much for your response. Actually, I need dielectric constant
= 4 for coulomb force. I have no idea where should I give 4. I thought
*epsilon-r:
() *will work for me . So If I use epsilon-rf: 4, it will work. am I
correct?

On Wed, Aug 16, 2017 at 8:52 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 8/15/17 9:22 PM, Mohammad Zahidul Hossain Khan wrote:
>
>> ; Dielectric constant (DC) for cut-off or DC of reaction field =
>> epsilon-r= 4
>>
>
> epsilon-r is used to change the relative dielectric constant; you
> shouldn't do this because it will fundamentally break the electrostatic
> convention used by all of the "usual" GROMACS force fields.
>
> If you're trying to alter reaction field properties, the keyword is
> epsilon-rf.  See the manual.
>
> -Justin
>
>
>> On Tue, Aug 15, 2017 at 6:18 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>> On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote:
>>>
>>> Dear Sir
>>>>
>>>> I am trying to simulate protein_ligand complex using epsilon = 4 and it
>>>> is
>>>> giving the below error
>>>>
>>>>
>>>> What is epsilon = 4?
>>>
>>> *2 particles communicated to PME rank 4 are more than 2/3 times the
>>> cut-off
>>>
>>>> out of the domain decomposition cell of their charge group in dimension
>>>> x*
>>>>
>>>> I have no idea how to solve this problem
>>>>
>>>>
>>>> Have you Googled it, or gone to the GROMACS error page, where lots of
>>> advice lives? ;)
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
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>>>
>>>
>>
>>
> --
> ==
>
> 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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-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*
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Re: [gmx-users] npt simulation error

2017-08-15 Thread Mohammad Zahidul Hossain Khan 
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r= 4


On Tue, Aug 15, 2017 at 6:18 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote:
>
>> Dear Sir
>>
>> I am trying to simulate protein_ligand complex using epsilon = 4 and it is
>> giving the below error
>>
>>
> What is epsilon = 4?
>
> *2 particles communicated to PME rank 4 are more than 2/3 times the cut-off
>> out of the domain decomposition cell of their charge group in dimension x*
>>
>> I have no idea how to solve this problem
>>
>>
> Have you Googled it, or gone to the GROMACS error page, where lots of
> advice lives? ;)
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
> --
> Gromacs Users mailing list
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>



-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*
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[gmx-users] npt simulation error

2017-08-15 Thread Mohammad Zahidul Hossain Khan 
Dear Sir

I am trying to simulate protein_ligand complex using epsilon = 4 and it is
giving the below error

*2 particles communicated to PME rank 4 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x*

I have no idea how to solve this problem
-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*
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[gmx-users] gmx sasa

2017-08-09 Thread Mohammad Zahidul Hossain Khan 
Dear Sir

Does anyone know how to measure the SASA energy with unit (kj/mol or
kcal/mol)

when i give this command:
*gmx sasa -f b.trr -s b.tpr -o b.xvg*
I got in Y-axix "Area (nm\S2\N)"

and when I give this command
*gmx sasa -f b.trr -s b.tpr -odg b.xvg*
I got in Y axix "D Gsolv"
but I do not know the unit.
-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
* Skype: parash.khan2*
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[gmx-users] error at nvt equilibrium

2017-08-04 Thread Mohammad Zahidul Hossain Khan 
Dear Sir

I am getting the error when I try for *gmx mdrun -deffnm nvt. *
I have attached my nvt.mdp. Can anyone help me about it

Double sids (1547, 1548) for atom 4837
Double sids (1547, 1548) for atom 4838
Double sids (1547, 1548) for atom 4839
Double sids (1547, 1548) for atom 4840
Double sids (1547, 1548) for atom 4841
Double sids (1547, 1548) for atom 4842
Double sids (1547, 1548) for atom 4843
Double sids (1547, 1548) for atom 4844
Double sids (1547, 1548) for atom 4845
Double sids (1547, 1548) for atom 4846
Double sids (1547, 1548) for atom 4847
Double sids (1547, 1548) for atom 4848
Double sids (1547, 1548) for atom 4849

---
Program gmx mdrun, VERSION 5.1.2
Source code file:
/build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/topology/invblock.c, line:
98

Fatal error:
Double entries in block structure. Item 3963 is in blocks 1548 and 1547
 Cannot make an unambiguous inverse block



-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
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Re: [gmx-users] Error in itp file

2017-08-03 Thread Mohammad Zahidul Hossain Khan 
write the ligand topology just after the forcefield parameter.

; Include forcefield parameters
#include "amber03.ff/forcefield.itp"

; Include ligand topology
#include "drg.itp"

On Thu, Aug 3, 2017 at 5:53 AM, Souvik Dey <souvik.de...@gmail.com> wrote:

> ​Yes, I saw the GROMACS website. But my itp file has [atomtypes] first
> followed by [moleculetypes]. So, I am still not getting what is the error.​
>
> On Thu, Aug 3, 2017 at 2:52 PM, Souvik Dey <souvik.de...@gmail.com> wrote:
>
> > Yes, using ACPYPE is pretty simple. They have a web server, where you can
> > upload your PDB or MOL2 file, provide the charge and multiplicity and it
> > gives you the output file.
> >
> > On Wed, Aug 2, 2017 at 7:03 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> >
> >>
> >>
> >> On 8/2/17 12:35 PM, Souvik Dey wrote:
> >>
> >>> Hi,
> >>>
> >>> I just generated an itp file from ACPYPE. However, if I try to add ions
> >>> it
> >>> shows the following error:
> >>>
> >>> Fatal error:
> >>> Syntax error - File FAD.itp, line 3
> >>> Last line read:
> >>> '[ atomtypes ]'
> >>> Invalid order for directive atomtypes
> >>>
> >>>
> >>> Can somebody say how do I fix this?
> >>>
> >>>
> >> This exact situation is described here:
> >>
> >> http://www.gromacs.org/Documentation/Errors#Invalid_order_fo
> >> r_directive_xxx
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support
> >> /Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
> >
> > --
> > Souvik Dey
> > Integrated Science Education & Research Centre
> > Visva Bharati University
> > Santiniketan-731235
> > West Bengal
> > 8981736643
> >
>
>
>
> --
> Souvik Dey
> Integrated Science Education & Research Centre
> Visva Bharati University
> Santiniketan-731235
> West Bengal
> 8981736643
> --
> Gromacs Users mailing list
>
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> send a mail to gmx-users-requ...@gromacs.org.




-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*
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Re: [gmx-users] Error in itp file

2017-08-03 Thread Mohammad Zahidul Hossain Khan 
Can you give web server link? I have tried but didn't find.

On Aug 3, 2017 5:53 AM, "Souvik Dey"  wrote:

> Yes, using ACPYPE is pretty simple. They have a web server, where you can
> upload your PDB or MOL2 file, provide the charge and multiplicity and it
> gives you the output file.
>
> On Wed, Aug 2, 2017 at 7:03 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 8/2/17 12:35 PM, Souvik Dey wrote:
> >
> >> Hi,
> >>
> >> I just generated an itp file from ACPYPE. However, if I try to add ions
> it
> >> shows the following error:
> >>
> >> Fatal error:
> >> Syntax error - File FAD.itp, line 3
> >> Last line read:
> >> '[ atomtypes ]'
> >> Invalid order for directive atomtypes
> >>
> >>
> >> Can somebody say how do I fix this?
> >>
> >>
> > This exact situation is described here:
> >
> > http://www.gromacs.org/Documentation/Errors#Invalid_order_
> > for_directive_xxx
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support
> > /Mailing_Lists/GMX-Users_List before posting!
> >
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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.
> >
>
>
>
> --
> Souvik Dey
> Integrated Science Education & Research Centre
> Visva Bharati University
> Santiniketan-731235
> West Bengal
> 8981736643
> --
> Gromacs Users mailing list
>
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Re: [gmx-users] Error in itp file

2017-08-02 Thread Mohammad Zahidul Hossain Khan 
Hi

Can you tell me, how have you used ACPYPE for itp.

On Aug 2, 2017 9:36 AM, "Souvik Dey"  wrote:

> Hi,
>
> I just generated an itp file from ACPYPE. However, if I try to add ions it
> shows the following error:
>
> Fatal error:
> Syntax error - File FAD.itp, line 3
> Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes
>
>
> Can somebody say how do I fix this?
>
> Regards,
> Souvik Dey
>
> --
> Souvik Dey
> Integrated Science Education & Research Centre
> Visva Bharati University
> Santiniketan-731235
> West Bengal
> 8981736643
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
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Re: [gmx-users] ligand topology

2017-08-01 Thread Mohammad Zahidul Hossain Khan 
I have found

However, if one wants *acpype* just to emulate *amb2gmx.pl*, one needs
nothing
at all but *[http://www.python.org Python]*.

At the moment, *acpype* is only available for download via *svn*:

  * `svn checkout http://acpype.googlecode.com/svn/trunk/ acpype`

Yet, if some reason you cannot use *svn*, one still can get *acpype* with:

  * `wget http://acpype.googlecode.com/svn/trunk/acpype.py`

But be aware that one may run in extra troubles and I am not willing to
support
this way.

== To Test ==

At folder *acpype/test*, type:

  * `../acpype.py -i FFF.pdb`

It'll create a folder called *FFF.acpype*, and inside it one may find
topology
files for GROMACS and CNS/XPLOR.


On Tue, Aug 1, 2017 at 3:00 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Have you read the acpype documentation before trying to use it?
>
> Mark
>
> On Tue, 1 Aug 2017 23:19 Mohammad Zahidul Hossain Khan <
> za.par...@gmail.com>
> wrote:
>
> > Dear Sir
> >
> > I have just use acpype.py -i OAI.pdb
> > I am getting the error:
> > ERROR: no 'antechamber' executable!
> > ERROR: no 'antechamber' executable... aborting !
> > ==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
> > ==> HINT2: is 'antechamber' in your $PATH?
> > What 'which antechamber' in your terminal says?
> > 'alias' doesn't work for ACPYPE.
> > ACPYPE FAILED: 1
> > Total time of execution: less than a second
> >
> > I am thinking that I have to install amber. But I dont want to do that.
> Is
> > there any way that I can create ligand topology for gaff.
> >
> >
> >
> > On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul <jalem...@vt.edu> wrote:
> >
> > >
> > >
> > > On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote:
> > >
> > >> Ok, you should not mix and match forcefields, ¿but in the case of
> > >> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter).
> > >>
> > >
> > > GAFF is compatible with AMBER (by design).  My comments were warning
> that
> > > one should not use AMBER for a protein in concert with GROMOS for a
> > ligand.
> > >
> > > -Justin
> > >
> > > Best regards.
> > >> Lucio Montero.
> > >>
> > >> Enviado desde Correo para Windows 10
> > >>
> > >> De: Alan
> > >> Enviado: martes, 1 de agosto de 2017 11:01 a. m.
> > >> Para: Gromacs
> > >> Asunto: Re: [gmx-users] ligand topology
> > >>
> > >> Please this GitHub link is totally outdated and not linked in any
> sense
> > to
> > >> the original authors.
> > >>
> > >> Get the correct ACPYPE here:
> > >>
> > >> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
> > >> stable/ccpn/python/acpype acpype
> > >>
> > >> On 1 August 2017 at 15:00, Suhaib Shekfeh <s.shek...@gmail.com>
> wrote:
> > >>
> > >> Actually, GAFF forcefield and amber forcefields are compatible. gaff
> is
> > >>> simply amber ff for small molecules.
> > >>> You have to get first amber tools. The last release is amber tools 16
> > >>> Get the source code from here :
> > >>> http://ambermd.org/AmberTools16-get.html
> > >>>
> > >>> after installation you can use antechamber for creating the
> > >>> small-molecule
> > >>> parameters
> > >>>
> > >>> later, you can use a nice free program called ACEPYP, made to convert
> > >>> amber
> > >>> parameters to gromacs toplogyget the code from here:
> > >>>
> > >>> https://github.com/t-/acpype
> > >>>
> > >>> Regards
> > >>>
> > >>>
> > >>>
> > >>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> > >>> za.par...@gmail.com> wrote:
> > >>>
> > >>> Dear Sir
> > >>>>
> > >>>> Thank you very much for your reply. Can you give me any link or
> > >>>>
> > >>> suggestion
> > >>>
> > >>>> that i can learn for amber force field for protein and ligand.
> > >>>>
> > >>>> On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul <jalem...@vt.edu>
> > wrote:
> > >>>>
> > >>>>
> > >>>>>
> > >>>>> On

Re: [gmx-users] ligand topology

2017-08-01 Thread Mohammad Zahidul Hossain Khan 
Dear Sir

I have just use acpype.py -i OAI.pdb
I am getting the error:
ERROR: no 'antechamber' executable!
ERROR: no 'antechamber' executable... aborting !
==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
==> HINT2: is 'antechamber' in your $PATH?
What 'which antechamber' in your terminal says?
'alias' doesn't work for ACPYPE.
ACPYPE FAILED: 1
Total time of execution: less than a second

I am thinking that I have to install amber. But I dont want to do that. Is
there any way that I can create ligand topology for gaff.



On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote:
>
>> Ok, you should not mix and match forcefields, ¿but in the case of
>> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter).
>>
>
> GAFF is compatible with AMBER (by design).  My comments were warning that
> one should not use AMBER for a protein in concert with GROMOS for a ligand.
>
> -Justin
>
> Best regards.
>> Lucio Montero.
>>
>> Enviado desde Correo para Windows 10
>>
>> De: Alan
>> Enviado: martes, 1 de agosto de 2017 11:01 a. m.
>> Para: Gromacs
>> Asunto: Re: [gmx-users] ligand topology
>>
>> Please this GitHub link is totally outdated and not linked in any sense to
>> the original authors.
>>
>> Get the correct ACPYPE here:
>>
>> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
>> stable/ccpn/python/acpype acpype
>>
>> On 1 August 2017 at 15:00, Suhaib Shekfeh <s.shek...@gmail.com> wrote:
>>
>> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
>>> simply amber ff for small molecules.
>>> You have to get first amber tools. The last release is amber tools 16
>>> Get the source code from here :
>>> http://ambermd.org/AmberTools16-get.html
>>>
>>> after installation you can use antechamber for creating the
>>> small-molecule
>>> parameters
>>>
>>> later, you can use a nice free program called ACEPYP, made to convert
>>> amber
>>> parameters to gromacs toplogyget the code from here:
>>>
>>> https://github.com/t-/acpype
>>>
>>> Regards
>>>
>>>
>>>
>>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
>>> za.par...@gmail.com> wrote:
>>>
>>> Dear Sir
>>>>
>>>> Thank you very much for your reply. Can you give me any link or
>>>>
>>> suggestion
>>>
>>>> that i can learn for amber force field for protein and ligand.
>>>>
>>>> On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>>>
>>>>
>>>>>
>>>>> On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
>>>>>
>>>>> Dear Sir
>>>>>>
>>>>>> I am new for protein-ligand complex. I want amber force field (ff03)
>>>>>>
>>>>> for
>>>
>>>> my
>>>>>> protein, tip3p for water model and gaff (General Amber force field)
>>>>>>
>>>>> for
>>>
>>>> ligand. I do not know how to produce gaff force field from pdb and
>>>>>>
>>>>> then
>>>
>>>> convert for gromacs topology.
>>>>>>
>>>>>> I have tried ff03 with gromos ligand topology and tip3p water model
>>>>>>
>>>>>> it gives me the error:
>>>>>> atomtype OM not found
>>>>>>
>>>>>> and when I have tried ff03 with gromos topology and spc water model it
>>>>>> gives me the error like:
>>>>>> atomtype HW not found.
>>>>>>
>>>>>> Can anyone help me about it?
>>>>>>
>>>>>>
>>>>>> You can't mix and match force fields; it's fundamentally wrong.  You
>>>>>
>>>> need
>>>
>>>> to develop ligand parameters that are consistent with the parent
>>>>>
>>>> protein
>>>
>>>> force field.  Various tools exist for different force fields, with
>>>>>
>>>> varying
>>>>
>>>>> degrees of reliability.
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==
>>>>>
>>>>> Just

Re: [gmx-users] ligand topology

2017-08-01 Thread Mohammad Zahidul Hossain Khan 
Dear Sir

Thank you very much.

On Tue, Aug 1, 2017 at 7:00 AM, Suhaib Shekfeh <s.shek...@gmail.com> wrote:

> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
> simply amber ff for small molecules.
> You have to get first amber tools. The last release is amber tools 16
> Get the source code from here :
> http://ambermd.org/AmberTools16-get.html
>
> after installation you can use antechamber for creating the small-molecule
> parameters
>
> later, you can use a nice free program called ACEPYP, made to convert amber
> parameters to gromacs toplogyget the code from here:
>
> https://github.com/t-/acpype
>
> Regards
>
>
>
> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> za.par...@gmail.com> wrote:
>
> > Dear Sir
> >
> > Thank you very much for your reply. Can you give me any link or
> suggestion
> > that i can learn for amber force field for protein and ligand.
> >
> > On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> >
> > >
> > >
> > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> > >
> > >> Dear Sir
> > >>
> > >> I am new for protein-ligand complex. I want amber force field (ff03)
> for
> > >> my
> > >> protein, tip3p for water model and gaff (General Amber force field)
> for
> > >> ligand. I do not know how to produce gaff force field from pdb and
> then
> > >> convert for gromacs topology.
> > >>
> > >> I have tried ff03 with gromos ligand topology and tip3p water model
> > >>
> > >> it gives me the error:
> > >> atomtype OM not found
> > >>
> > >> and when I have tried ff03 with gromos topology and spc water model it
> > >> gives me the error like:
> > >> atomtype HW not found.
> > >>
> > >> Can anyone help me about it?
> > >>
> > >>
> > > You can't mix and match force fields; it's fundamentally wrong.  You
> need
> > > to develop ligand parameters that are consistent with the parent
> protein
> > > force field.  Various tools exist for different force fields, with
> > varying
> > > degrees of reliability.
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/Support
> > > /Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * 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.
> > >
> >
> >
> >
> > --
> >
> >
> > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
> > *Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
> > * Skype: parash.khan2*
> > *Cell: +12085967165*
> > --
> > 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.
> >
>
>
>
> --
> Dr. rer. nat. Suhaib Shekfeh
> PhD in Computational Drug Design and Medicinal Chemistry
> Oleariusstr. 11, Halle (Saale), Germany
> LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255
> --
> 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.
>



-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*
-- 
Gromacs Users mailing list

* Please search the archive at 
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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Re: [gmx-users] ligand topology

2017-07-31 Thread Mohammad Zahidul Hossain Khan 
Dear Sir

Thank you very much for your reply. Can you give me any link or suggestion
that i can learn for amber force field for protein and ligand.

On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
>
>> Dear Sir
>>
>> I am new for protein-ligand complex. I want amber force field (ff03) for
>> my
>> protein, tip3p for water model and gaff (General Amber force field) for
>> ligand. I do not know how to produce gaff force field from pdb and then
>> convert for gromacs topology.
>>
>> I have tried ff03 with gromos ligand topology and tip3p water model
>>
>> it gives me the error:
>> atomtype OM not found
>>
>> and when I have tried ff03 with gromos topology and spc water model it
>> gives me the error like:
>> atomtype HW not found.
>>
>> Can anyone help me about it?
>>
>>
> You can't mix and match force fields; it's fundamentally wrong.  You need
> to develop ligand parameters that are consistent with the parent protein
> force field.  Various tools exist for different force fields, with varying
> degrees of reliability.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * 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.
>



-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*
-- 
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* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] ligand topology

2017-07-31 Thread Mohammad Zahidul Hossain Khan 
Dear Sir

I am new for protein-ligand complex. I want amber force field (ff03) for my
protein, tip3p for water model and gaff (General Amber force field) for
ligand. I do not know how to produce gaff force field from pdb and then
convert for gromacs topology.

I have tried ff03 with gromos ligand topology and tip3p water model

it gives me the error:
atomtype OM not found

and when I have tried ff03 with gromos topology and spc water model it
gives me the error like:
atomtype HW not found.

Can anyone help me about it?

-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] energy minization mdp

2017-07-29 Thread Mohammad Zahidul Hossain Khan 
Dear Sir

Thank you very much. It is working now.



On Fri, Jul 28, 2017 at 4:16 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 7/28/17 2:54 PM, Mohammad Zahidul Hossain Khan wrote:
>
>> Dear User
>>
>> I have protein-ligand system. I have basic idea for energy
>> minimization.mdp
>> parameter.
>> ;
>> integrator = steep
>> emtol = 10.0
>> emstep = 0.01
>> nsteps = 500
>> energygrps = Protein OAI
>> ;
>> nstlist= 1
>> cutoff-scheme = Verlet
>> ns_type= grid
>> rlist= 1.0
>> coulombtype= PME
>> rcoulomb= 1.0
>> rvdw= 1.0
>> pbc= xyz
>>
>> but I have not idea how to write the parameter *where all the backbone
>> heavy atoms of the protein have to be constrained with an elastic constant
>> of 50 kcal /mol Å -2 and the other atoms should be free.*
>>
>> Does anyone know how to write elastic constant parameter in energy
>> minimization mdp file.
>>
>>
> Restraints are a topological construct, not one that is (directly)
> specified in the .mdp file.  Run your protein coordinates (only) through
> gmx genrestr and choose the backbone as the output group.  Specify the
> desired force constant on the command line (make sure to convert your value
> to kJ mol^-1 nm^-2).  Save the new position restraint file to something
> like "posre_bb.itp" and #include it in the topology in the protein's
> [moleculetype] section, e.g.
>
> #ifdef POSRES_BB
> #include "posre_bb.itp"
> #endif
>
> Then specify "define = -DPOSRES_BB" in the .mdp file.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * 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.




-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*
-- 
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] energy minization mdp

2017-07-28 Thread Mohammad Zahidul Hossain Khan 
Dear User

I have protein-ligand system. I have basic idea for energy minimization.mdp
parameter.
;
integrator = steep
emtol = 10.0
emstep = 0.01
nsteps = 500
energygrps = Protein OAI
;
nstlist= 1
cutoff-scheme = Verlet
ns_type= grid
rlist= 1.0
coulombtype= PME
rcoulomb= 1.0
rvdw= 1.0
pbc= xyz

but I have not idea how to write the parameter *where all the backbone
heavy atoms of the protein have to be constrained with an elastic constant
of 50 kcal /mol Å -2 and the other atoms should be free.*

Does anyone know how to write elastic constant parameter in energy
minimization mdp file.

-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*
-- 
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