Re: [gmx-users] Regarding gromacs commands..

[Mark Abraham]

Hi,

I mean in this thread

Mark

On Mon, Jan 9, 2017 at 7:16 PM Thomas Allen  wrote:

> Which thread do you mean? I'd be happy to take a look, but I'm new to
> the mailing list and having some trouble finding the right search
> keywords for the archive.
>
> -Tom
>
> Quoting Mark Abraham :
>
> > Hi,
> >
> > Justin suggested a useful procedure a few emails back. Have you tried it?
> >
> > Mark
> >
> > On Mon, 9 Jan 2017 17:36 Dilip H N  wrote:
> >
> >> Sir, i want to run an simulation of 300 molecules of ammonia...
> >> how can i proceed with it..??
> >> can u please help me out
> >>
> >>
> >>
> >>  Sent with Mailtrack
> >> <
> >>
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22
> >> >
> >>
> >> On Mon, Jan 9, 2017 at 9:37 AM, Dilip H N 
> >> wrote:
> >>
> >> > 1] I want to simulate ammonia.
> >> > 2] if i am creating in the avogadro molecular editor for 216
> molecules of
> >> > ammonia.. it is not writing the residue no. ie., for 1 NH3, it should
> >> write
> >> > (4atoms),next NH3 ..., and in this file below, the z axis is
> >> almost
> >> > same...ie., 50.037,49.75how can i alter the z axis
> >> > 3]i tired to generate the topology from the perl interprter
> >> > 4] gmx grompp -f file.mdp -c file.gro -p file.top
> >> > 5] gmx mdrun -v deffnm em -s file.tpr
> >> > and it gace me segmentation error
> >> > here is the .mdp file, .pdb file
> >> >
> >> >
> >> >
> >> >  Sent with Mailtrack
> >> > <
> >>
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22
> >> >
> >> >
> >> > On Sun, Jan 8, 2017 at 10:22 PM, Justin Lemkul 
> wrote:
> >> >
> >> >>
> >> >>
> >> >> On 1/7/17 10:58 PM, Dilip H N wrote:
> >> >>
> >> >>> can i create it with Avogadro molecular editor software..??
> >> >>>
> >> >>
> >> >> Probably, but that's a question for whatever help forum they provide.
> >> >>
> >> >> I tried creating using this software,, than if i compile it and run
> the
> >> >>> command of mdrun..
> >> >>> it is giving segmentation fault
> >> >>> how to rectify it..??
> >> >>>
> >> >>>
> >> >> Not a clue.  There are a ton of steps between "create a PDB file" and
> >> >> "execute mdrun," none of which you've shown us.  If you want detailed
> >> help,
> >> >> you have to provide detailed information (steps taken, exact commands
> >> >> given, text of input files and what you're trying to accomplish,
> etc).
> >> We
> >> >> can't read your mind.  A seg fault is a catastrophic failure of the
> >> >> physical model due to problems with any number of things.  It's not
> >> >> productive for anyone to guess.
> >> >>
> >> >>
> >> >> -Justin
> >> >>
> >> >>
> >> >>>
> >> >>>  Sent with Mailtrack
> >> >>>  >> >>> ral=cy16f01.di...@nitk.edu.in&idSignature=22>
> >> >>>
> >> >>> On Sat, Jan 7, 2017 at 12:15 AM, Justin Lemkul 
> >> wrote:
> >> >>>
> >> >>>
> >> 
> >>  On 1/6/17 2:24 AM, Dilip H N wrote:
> >> 
> >>  no...
> >> > I want to create  300 molecules of ammonia...
> >> >
> >> >
> >>  Well, you asked about BF3, so you got an answer about BF3 :)
> >> 
> >>  how can i create  300 molecules of ammonia and then get it in .pdb
> >> file
> >> 
> >> > format..??
> >> >
> >> >
> >> > For a simple molecule like NH3 you can easily write the
> coordinates
> >> by
> >>  hand from basic geometry.  Otherwise, find an NMR structure of a
> >> protein
> >>  that contains Lys and copy its NZ-HZ[123] group and use that.  gmx
> >>  insert-molecules -nmol 300 will give you a box of 300.
> >> 
> >>  -Justin
> >> 
> >> 
> >> 
> >> >  Sent with Mailtrack
> >> >  >> > ral=cy16f01.di...@nitk.edu.in&idSignature=22>
> >> >
> >> > On Fri, Jan 6, 2017 at 11:01 AM, Alex 
> wrote:
> >> >
> >> > Google "bf3 rcsb" > third result from the top
> >> >
> >> >> https://www3.rcsb.org/ligand/BF3 > download cif file
> (view/download
> >> >> on
> >> >> the right) > open in pymol > save as pdb
> >> >>
> >> >> Alex
> >> >>
> >> >>
> >> >> On 1/5/2017 10:20 PM, Dilip H N wrote:
> >> >>
> >> >> I want to do a simulation of BF3 molecule..
> >> >>
> >> >>> how can i create a pdb file of BF3 molecule..??
> >> >>> is there any softwares for creating a .pdb files ..??
> >> >>>
> >> >>>
> >> >>>
> >> >>> --
> >> >>>
> >> >> 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
> >> 

Re: [gmx-users] Regarding gromacs commands..

[Thomas Allen]

Which thread do you mean? I'd be happy to take a look, but I'm new to  
the mailing list and having some trouble finding the right search  
keywords for the archive.


-Tom

Quoting Mark Abraham :


Hi,

Justin suggested a useful procedure a few emails back. Have you tried it?

Mark

On Mon, 9 Jan 2017 17:36 Dilip H N  wrote:


Sir, i want to run an simulation of 300 molecules of ammonia...
how can i proceed with it..??
can u please help me out



 Sent with Mailtrack
<
https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22
>

On Mon, Jan 9, 2017 at 9:37 AM, Dilip H N 
wrote:

> 1] I want to simulate ammonia.
> 2] if i am creating in the avogadro molecular editor for 216 molecules of
> ammonia.. it is not writing the residue no. ie., for 1 NH3, it should
write
> (4atoms),next NH3 ..., and in this file below, the z axis is
almost
> same...ie., 50.037,49.75how can i alter the z axis
> 3]i tired to generate the topology from the perl interprter
> 4] gmx grompp -f file.mdp -c file.gro -p file.top
> 5] gmx mdrun -v deffnm em -s file.tpr
> and it gace me segmentation error
> here is the .mdp file, .pdb file
>
>
>
>  Sent with Mailtrack
> <
https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22
>
>
> On Sun, Jan 8, 2017 at 10:22 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 1/7/17 10:58 PM, Dilip H N wrote:
>>
>>> can i create it with Avogadro molecular editor software..??
>>>
>>
>> Probably, but that's a question for whatever help forum they provide.
>>
>> I tried creating using this software,, than if i compile it and run the
>>> command of mdrun..
>>> it is giving segmentation fault
>>> how to rectify it..??
>>>
>>>
>> Not a clue.  There are a ton of steps between "create a PDB file" and
>> "execute mdrun," none of which you've shown us.  If you want detailed
help,
>> you have to provide detailed information (steps taken, exact commands
>> given, text of input files and what you're trying to accomplish, etc).
We
>> can't read your mind.  A seg fault is a catastrophic failure of the
>> physical model due to problems with any number of things.  It's not
>> productive for anyone to guess.
>>
>>
>> -Justin
>>
>>
>>>
>>>  Sent with Mailtrack
>>> >> ral=cy16f01.di...@nitk.edu.in&idSignature=22>
>>>
>>> On Sat, Jan 7, 2017 at 12:15 AM, Justin Lemkul 
wrote:
>>>
>>>

 On 1/6/17 2:24 AM, Dilip H N wrote:

 no...
> I want to create  300 molecules of ammonia...
>
>
 Well, you asked about BF3, so you got an answer about BF3 :)

 how can i create  300 molecules of ammonia and then get it in .pdb
file

> format..??
>
>
> For a simple molecule like NH3 you can easily write the coordinates
by
 hand from basic geometry.  Otherwise, find an NMR structure of a
protein
 that contains Lys and copy its NZ-HZ[123] group and use that.  gmx
 insert-molecules -nmol 300 will give you a box of 300.

 -Justin



>  Sent with Mailtrack
>  ral=cy16f01.di...@nitk.edu.in&idSignature=22>
>
> On Fri, Jan 6, 2017 at 11:01 AM, Alex  wrote:
>
> Google "bf3 rcsb" > third result from the top
>
>> https://www3.rcsb.org/ligand/BF3 > download cif file (view/download
>> on
>> the right) > open in pymol > save as pdb
>>
>> Alex
>>
>>
>> On 1/5/2017 10:20 PM, Dilip H N wrote:
>>
>> I want to do a simulation of BF3 molecule..
>>
>>> how can i create a pdb file of BF3 molecule..??
>>> is there any softwares for creating a .pdb files ..??
>>>
>>>
>>>
>>> --
>>>
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>>
>>
>
>
> --
 ==

 Justin A. Lemkul, Ph.D.
 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.gromac

Re: [gmx-users] Regarding gromacs commands..

[Mark Abraham]

Hi,

Justin suggested a useful procedure a few emails back. Have you tried it?

Mark

On Mon, 9 Jan 2017 17:36 Dilip H N  wrote:

> Sir, i want to run an simulation of 300 molecules of ammonia...
> how can i proceed with it..??
> can u please help me out
>
>
>
>  Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22
> >
>
> On Mon, Jan 9, 2017 at 9:37 AM, Dilip H N 
> wrote:
>
> > 1] I want to simulate ammonia.
> > 2] if i am creating in the avogadro molecular editor for 216 molecules of
> > ammonia.. it is not writing the residue no. ie., for 1 NH3, it should
> write
> > (4atoms),next NH3 ..., and in this file below, the z axis is
> almost
> > same...ie., 50.037,49.75how can i alter the z axis
> > 3]i tired to generate the topology from the perl interprter
> > 4] gmx grompp -f file.mdp -c file.gro -p file.top
> > 5] gmx mdrun -v deffnm em -s file.tpr
> > and it gace me segmentation error
> > here is the .mdp file, .pdb file
> >
> >
> >
> >  Sent with Mailtrack
> > <
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22
> >
> >
> > On Sun, Jan 8, 2017 at 10:22 PM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 1/7/17 10:58 PM, Dilip H N wrote:
> >>
> >>> can i create it with Avogadro molecular editor software..??
> >>>
> >>
> >> Probably, but that's a question for whatever help forum they provide.
> >>
> >> I tried creating using this software,, than if i compile it and run the
> >>> command of mdrun..
> >>> it is giving segmentation fault
> >>> how to rectify it..??
> >>>
> >>>
> >> Not a clue.  There are a ton of steps between "create a PDB file" and
> >> "execute mdrun," none of which you've shown us.  If you want detailed
> help,
> >> you have to provide detailed information (steps taken, exact commands
> >> given, text of input files and what you're trying to accomplish, etc).
> We
> >> can't read your mind.  A seg fault is a catastrophic failure of the
> >> physical model due to problems with any number of things.  It's not
> >> productive for anyone to guess.
> >>
> >>
> >> -Justin
> >>
> >>
> >>>
> >>>  Sent with Mailtrack
> >>>  >>> ral=cy16f01.di...@nitk.edu.in&idSignature=22>
> >>>
> >>> On Sat, Jan 7, 2017 at 12:15 AM, Justin Lemkul 
> wrote:
> >>>
> >>>
> 
>  On 1/6/17 2:24 AM, Dilip H N wrote:
> 
>  no...
> > I want to create  300 molecules of ammonia...
> >
> >
>  Well, you asked about BF3, so you got an answer about BF3 :)
> 
>  how can i create  300 molecules of ammonia and then get it in .pdb
> file
> 
> > format..??
> >
> >
> > For a simple molecule like NH3 you can easily write the coordinates
> by
>  hand from basic geometry.  Otherwise, find an NMR structure of a
> protein
>  that contains Lys and copy its NZ-HZ[123] group and use that.  gmx
>  insert-molecules -nmol 300 will give you a box of 300.
> 
>  -Justin
> 
> 
> 
> >  Sent with Mailtrack
> >  > ral=cy16f01.di...@nitk.edu.in&idSignature=22>
> >
> > On Fri, Jan 6, 2017 at 11:01 AM, Alex  wrote:
> >
> > Google "bf3 rcsb" > third result from the top
> >
> >> https://www3.rcsb.org/ligand/BF3 > download cif file (view/download
> >> on
> >> the right) > open in pymol > save as pdb
> >>
> >> Alex
> >>
> >>
> >> On 1/5/2017 10:20 PM, Dilip H N wrote:
> >>
> >> I want to do a simulation of BF3 molecule..
> >>
> >>> how can i create a pdb file of BF3 molecule..??
> >>> is there any softwares for creating a .pdb files ..??
> >>>
> >>>
> >>>
> >>> --
> >>>
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support
> >> /Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >>
> >>
> >
> >
> > --
>  ==
> 
>  Justin A. Lemkul, Ph.D.
>  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:

Re: [gmx-users] Regarding gromacs commands..

[Dilip H N]

Sir, i want to run an simulation of 300 molecules of ammonia...
how can i proceed with it..??
can u please help me out



 Sent with Mailtrack


On Mon, Jan 9, 2017 at 9:37 AM, Dilip H N  wrote:

> 1] I want to simulate ammonia.
> 2] if i am creating in the avogadro molecular editor for 216 molecules of
> ammonia.. it is not writing the residue no. ie., for 1 NH3, it should write
> (4atoms),next NH3 ..., and in this file below, the z axis is almost
> same...ie., 50.037,49.75how can i alter the z axis
> 3]i tired to generate the topology from the perl interprter
> 4] gmx grompp -f file.mdp -c file.gro -p file.top
> 5] gmx mdrun -v deffnm em -s file.tpr
> and it gace me segmentation error
> here is the .mdp file, .pdb file
>
>
>
>  Sent with Mailtrack
> 
>
> On Sun, Jan 8, 2017 at 10:22 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 1/7/17 10:58 PM, Dilip H N wrote:
>>
>>> can i create it with Avogadro molecular editor software..??
>>>
>>
>> Probably, but that's a question for whatever help forum they provide.
>>
>> I tried creating using this software,, than if i compile it and run the
>>> command of mdrun..
>>> it is giving segmentation fault
>>> how to rectify it..??
>>>
>>>
>> Not a clue.  There are a ton of steps between "create a PDB file" and
>> "execute mdrun," none of which you've shown us.  If you want detailed help,
>> you have to provide detailed information (steps taken, exact commands
>> given, text of input files and what you're trying to accomplish, etc).  We
>> can't read your mind.  A seg fault is a catastrophic failure of the
>> physical model due to problems with any number of things.  It's not
>> productive for anyone to guess.
>>
>>
>> -Justin
>>
>>
>>>
>>>  Sent with Mailtrack
>>> >> ral=cy16f01.di...@nitk.edu.in&idSignature=22>
>>>
>>> On Sat, Jan 7, 2017 at 12:15 AM, Justin Lemkul  wrote:
>>>
>>>

 On 1/6/17 2:24 AM, Dilip H N wrote:

 no...
> I want to create  300 molecules of ammonia...
>
>
 Well, you asked about BF3, so you got an answer about BF3 :)

 how can i create  300 molecules of ammonia and then get it in .pdb file

> format..??
>
>
> For a simple molecule like NH3 you can easily write the coordinates by
 hand from basic geometry.  Otherwise, find an NMR structure of a protein
 that contains Lys and copy its NZ-HZ[123] group and use that.  gmx
 insert-molecules -nmol 300 will give you a box of 300.

 -Justin



>  Sent with Mailtrack
>  ral=cy16f01.di...@nitk.edu.in&idSignature=22>
>
> On Fri, Jan 6, 2017 at 11:01 AM, Alex  wrote:
>
> Google "bf3 rcsb" > third result from the top
>
>> https://www3.rcsb.org/ligand/BF3 > download cif file (view/download
>> on
>> the right) > open in pymol > save as pdb
>>
>> Alex
>>
>>
>> On 1/5/2017 10:20 PM, Dilip H N wrote:
>>
>> I want to do a simulation of BF3 molecule..
>>
>>> how can i create a pdb file of BF3 molecule..??
>>> is there any softwares for creating a .pdb files ..??
>>>
>>>
>>>
>>> --
>>>
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>>
>>
>
>
> --
 ==

 Justin A. Lemkul, Ph.D.
 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.


>>>
>>>
>>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein

Re: [gmx-users] Regarding gromacs commands..

[Justin Lemkul]

On 1/7/17 10:58 PM, Dilip H N wrote:

can i create it with Avogadro molecular editor software..??


Probably, but that's a question for whatever help forum they provide.


I tried creating using this software,, than if i compile it and run the
command of mdrun..
it is giving segmentation fault
how to rectify it..??



Not a clue.  There are a ton of steps between "create a PDB file" and "execute 
mdrun," none of which you've shown us.  If you want detailed help, you have to 
provide detailed information (steps taken, exact commands given, text of input 
files and what you're trying to accomplish, etc).  We can't read your mind.  A 
seg fault is a catastrophic failure of the physical model due to problems with 
any number of things.  It's not productive for anyone to guess.


-Justin




 Sent with Mailtrack


On Sat, Jan 7, 2017 at 12:15 AM, Justin Lemkul  wrote:




On 1/6/17 2:24 AM, Dilip H N wrote:


no...
I want to create  300 molecules of ammonia...



Well, you asked about BF3, so you got an answer about BF3 :)

how can i create  300 molecules of ammonia and then get it in .pdb file

format..??



For a simple molecule like NH3 you can easily write the coordinates by
hand from basic geometry.  Otherwise, find an NMR structure of a protein
that contains Lys and copy its NZ-HZ[123] group and use that.  gmx
insert-molecules -nmol 300 will give you a box of 300.

-Justin




 Sent with Mailtrack


On Fri, Jan 6, 2017 at 11:01 AM, Alex  wrote:

Google "bf3 rcsb" > third result from the top

https://www3.rcsb.org/ligand/BF3 > download cif file (view/download on
the right) > open in pymol > save as pdb

Alex


On 1/5/2017 10:20 PM, Dilip H N wrote:

I want to do a simulation of BF3 molecule..

how can i create a pdb file of BF3 molecule..??
is there any softwares for creating a .pdb files ..??



--

Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.







--
==

Justin A. Lemkul, Ph.D.
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.







--
==

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.

Re: [gmx-users] Regarding gromacs commands..

[Dilip H N]

can i create it with Avogadro molecular editor software..??
I tried creating using this software,, than if i compile it and run the
command of mdrun..
it is giving segmentation fault
how to rectify it..??



 Sent with Mailtrack


On Sat, Jan 7, 2017 at 12:15 AM, Justin Lemkul  wrote:

>
>
> On 1/6/17 2:24 AM, Dilip H N wrote:
>
>> no...
>> I want to create  300 molecules of ammonia...
>>
>
> Well, you asked about BF3, so you got an answer about BF3 :)
>
> how can i create  300 molecules of ammonia and then get it in .pdb file
>> format..??
>>
>>
> For a simple molecule like NH3 you can easily write the coordinates by
> hand from basic geometry.  Otherwise, find an NMR structure of a protein
> that contains Lys and copy its NZ-HZ[123] group and use that.  gmx
> insert-molecules -nmol 300 will give you a box of 300.
>
> -Justin
>
>
>>
>>  Sent with Mailtrack
>> > ral=cy16f01.di...@nitk.edu.in&idSignature=22>
>>
>> On Fri, Jan 6, 2017 at 11:01 AM, Alex  wrote:
>>
>> Google "bf3 rcsb" > third result from the top
>>> https://www3.rcsb.org/ligand/BF3 > download cif file (view/download on
>>> the right) > open in pymol > save as pdb
>>>
>>> Alex
>>>
>>>
>>> On 1/5/2017 10:20 PM, Dilip H N wrote:
>>>
>>> I want to do a simulation of BF3 molecule..
 how can i create a pdb file of BF3 molecule..??
 is there any softwares for creating a .pdb files ..??



 --
>>> 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.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
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> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student,
Research Scholar,
Department of Chemistry,
National Institute of Technology-Karnataka,
Surathkal, Mangaluru - 575025.
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Re: [gmx-users] Regarding gromacs commands..

[Justin Lemkul]

On 1/6/17 2:24 AM, Dilip H N wrote:

no...
I want to create  300 molecules of ammonia...


Well, you asked about BF3, so you got an answer about BF3 :)


how can i create  300 molecules of ammonia and then get it in .pdb file
format..??



For a simple molecule like NH3 you can easily write the coordinates by hand from 
basic geometry.  Otherwise, find an NMR structure of a protein that contains Lys 
and copy its NZ-HZ[123] group and use that.  gmx insert-molecules -nmol 300 will 
give you a box of 300.


-Justin




 Sent with Mailtrack


On Fri, Jan 6, 2017 at 11:01 AM, Alex  wrote:


Google "bf3 rcsb" > third result from the top
https://www3.rcsb.org/ligand/BF3 > download cif file (view/download on
the right) > open in pymol > save as pdb

Alex


On 1/5/2017 10:20 PM, Dilip H N wrote:


I want to do a simulation of BF3 molecule..
how can i create a pdb file of BF3 molecule..??
is there any softwares for creating a .pdb files ..??




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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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* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.







--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Regarding gromacs commands..

[Dilip H N]

no...
I want to create  300 molecules of ammonia...
how can i create  300 molecules of ammonia and then get it in .pdb file
format..??



 Sent with Mailtrack


On Fri, Jan 6, 2017 at 11:01 AM, Alex  wrote:

> Google "bf3 rcsb" > third result from the top
> https://www3.rcsb.org/ligand/BF3 > download cif file (view/download on
> the right) > open in pymol > save as pdb
>
> Alex
>
>
> On 1/5/2017 10:20 PM, Dilip H N wrote:
>
>> I want to do a simulation of BF3 molecule..
>> how can i create a pdb file of BF3 molecule..??
>> is there any softwares for creating a .pdb files ..??
>>
>>
>>
> --
> 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.
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student,
Research Scholar,
Department of Chemistry,
National Institute of Technology-Karnataka,
Surathkal, Mangaluru - 575025.
-- 
Gromacs Users mailing list

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Re: [gmx-users] Regarding gromacs commands..

[Alex]

Google "bf3 rcsb" > third result from the top 
https://www3.rcsb.org/ligand/BF3 > download cif file (view/download on 
the right) > open in pymol > save as pdb


Alex

On 1/5/2017 10:20 PM, Dilip H N wrote:

I want to do a simulation of BF3 molecule..
how can i create a pdb file of BF3 molecule..??
is there any softwares for creating a .pdb files ..??




--
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Re: [gmx-users] Regarding gromacs commands..

[Dilip H N]

I want to do a simulation of BF3 molecule..
how can i create a pdb file of BF3 molecule..??
is there any softwares for creating a .pdb files ..??



 Sent with Mailtrack


On Thu, Jan 5, 2017 at 11:12 PM, Dilip H N 
wrote:

> In argon simulation why have they used -nice o at the end command during
> compilation..??
> ie.,
> gmx mdrun -s topol.tpr -v -c argon_1ns.gro -nice 0
> what is the need of it ...
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student,
> Research Scholar,
> Department of Chemistry,
> National Institute of Technology-Karnataka,
> Surathkal, Mangaluru - 575025.
>
>
>
>  Sent with Mailtrack
> 
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student,
Research Scholar,
Department of Chemistry,
National Institute of Technology-Karnataka,
Surathkal, Mangaluru - 575025.
-- 
Gromacs Users mailing list

* Please search the archive at 
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* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Regarding gromacs commands..

[Dilip H N]

In argon simulation why have they used -nice o at the end command during
compilation..??
ie.,
gmx mdrun -s topol.tpr -v -c argon_1ns.gro -nice 0
what is the need of it ...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student,
Research Scholar,
Department of Chemistry,
National Institute of Technology-Karnataka,
Surathkal, Mangaluru - 575025.



 Sent with Mailtrack

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