date:20170225

Re: [gmx-users] GRO File Merging

2017-02-25 Thread Mark Abraham

Hi,

Sure the process is reasonable, but clearly you got some detail wrong :-)

Mark

On Sat, 25 Feb 2017 21:10 Sanim Rahman  wrote:

> Hello Mark,
>
> I was able to get around the issue so no worries. The reason why I split
> them up because I wanted to describe my lipids in CHARMM36 parameters and
> protein in CHARMM27 in order to replicate a simulation.
>
> However, is my thought process for the topology file correct?
>
> Regards,
>
> *Sanim Rahman*
> B.S. Chemical Engineering, 2019
> Resident Assistant, Castor Hall Engineering Living Learning Community
> 2016-2017
> Co-Founder and Co-President of the Undergraduate Research Society
> Undergraduate Researcher, Global Center for Hearing and Speech Research
> 
>
>
> On Sat, Feb 25, 2017 at 2:59 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Why are you splitting things up? The whole coordinate file from charmm
> gui
> > is the useful thing.
> >
> > Mark
> >
> > On Sat, 25 Feb 2017 20:21 Sanim Rahman  wrote:
> >
> > > Hi all,
> > >
> > > I have been using gromacs to design a membrane protein system. I used
> > > CHARMM-GUI to design my membrane and then was able to split my system
> > into
> > > three parts (protein, lipid, solvent) and convert it into .gro format.
> I
> > am
> > > able to individually view each part in VMD all together but when I use:
> > >
> > > *cat protein.gro lipid.gro solvent.gro > system.gro*
> > >
> > > The molecule does not show up in VMD. I properly edit the number of
> atoms
> > > and the box coordinates of the system by using -editconf to correct the
> > box
> > > coordinates. I receive no errors in VMD as well. What should I do to
> fix
> > > this?
> > >
> > > Also when combining topology files, I would convert lipid.top and
> > > solvent.top into .itp files and use the #include statement to combine
> > them
> > > into my protein.top file? After that, my system should be set correct?
> > >
> > > Thank You,
> > > Sanim Rahman
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > >
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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> >
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Re: [gmx-users] GRO File Merging

2017-02-25 Thread Sanim Rahman

Hello Mark,

I was able to get around the issue so no worries. The reason why I split
them up because I wanted to describe my lipids in CHARMM36 parameters and
protein in CHARMM27 in order to replicate a simulation.

However, is my thought process for the topology file correct?

Regards,

*Sanim Rahman*
B.S. Chemical Engineering, 2019
Resident Assistant, Castor Hall Engineering Living Learning Community
2016-2017
Co-Founder and Co-President of the Undergraduate Research Society
Undergraduate Researcher, Global Center for Hearing and Speech Research

On Sat, Feb 25, 2017 at 2:59 PM, Mark Abraham 
wrote:

> Hi,
>
> Why are you splitting things up? The whole coordinate file from charmm gui
> is the useful thing.
>
> Mark
>
> On Sat, 25 Feb 2017 20:21 Sanim Rahman  wrote:
>
> > Hi all,
> >
> > I have been using gromacs to design a membrane protein system. I used
> > CHARMM-GUI to design my membrane and then was able to split my system
> into
> > three parts (protein, lipid, solvent) and convert it into .gro format. I
> am
> > able to individually view each part in VMD all together but when I use:
> >
> > *cat protein.gro lipid.gro solvent.gro > system.gro*
> >
> > The molecule does not show up in VMD. I properly edit the number of atoms
> > and the box coordinates of the system by using -editconf to correct the
> box
> > coordinates. I receive no errors in VMD as well. What should I do to fix
> > this?
> >
> > Also when combining topology files, I would convert lipid.top and
> > solvent.top into .itp files and use the #include statement to combine
> them
> > into my protein.top file? After that, my system should be set correct?
> >
> > Thank You,
> > Sanim Rahman
> > --
> > 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
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>
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Re: [gmx-users] GRO File Merging

2017-02-25 Thread Mark Abraham

Hi,

Why are you splitting things up? The whole coordinate file from charmm gui
is the useful thing.

Mark

On Sat, 25 Feb 2017 20:21 Sanim Rahman  wrote:

> Hi all,
>
> I have been using gromacs to design a membrane protein system. I used
> CHARMM-GUI to design my membrane and then was able to split my system into
> three parts (protein, lipid, solvent) and convert it into .gro format. I am
> able to individually view each part in VMD all together but when I use:
>
> *cat protein.gro lipid.gro solvent.gro > system.gro*
>
> The molecule does not show up in VMD. I properly edit the number of atoms
> and the box coordinates of the system by using -editconf to correct the box
> coordinates. I receive no errors in VMD as well. What should I do to fix
> this?
>
> Also when combining topology files, I would convert lipid.top and
> solvent.top into .itp files and use the #include statement to combine them
> into my protein.top file? After that, my system should be set correct?
>
> Thank You,
> Sanim Rahman
> --
> 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] GRO File Merging

2017-02-25 Thread Sanim Rahman

Hi all,

I have been using gromacs to design a membrane protein system. I used
CHARMM-GUI to design my membrane and then was able to split my system into
three parts (protein, lipid, solvent) and convert it into .gro format. I am
able to individually view each part in VMD all together but when I use:

*cat protein.gro lipid.gro solvent.gro > system.gro*

The molecule does not show up in VMD. I properly edit the number of atoms
and the box coordinates of the system by using -editconf to correct the box
coordinates. I receive no errors in VMD as well. What should I do to fix
this?

Also when combining topology files, I would convert lipid.top and
solvent.top into .itp files and use the #include statement to combine them
into my protein.top file? After that, my system should be set correct?

Thank You,
Sanim Rahman
-- 
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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Re: [gmx-users] Adding a number of drugs around a polymer

2017-02-25 Thread Tasneem Kausar

Check gmx insert

On 25 Feb 2017 18:12, "faride badalkhani"  wrote:

> Dear GROMACS users,
>
> I need to locate a number of drug molecules around one equilibrated polymer
> molecule and drugs should be randomly located within a spherical shell from
> the polymer surface.
> Will be greatly appreciated if help me on that.
>
> Regards,
> Farideh
> --
> 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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[gmx-users] Adding a number of drugs around a polymer

2017-02-25 Thread faride badalkhani

Dear GROMACS users,

I need to locate a number of drug molecules around one equilibrated polymer
molecule and drugs should be randomly located within a spherical shell from
the polymer surface.
Will be greatly appreciated if help me on that.

Regards,
Farideh
-- 
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Re: [gmx-users] GRO File Merging

Re: [gmx-users] GRO File Merging

Re: [gmx-users] GRO File Merging

[gmx-users] GRO File Merging

Re: [gmx-users] Adding a number of drugs around a polymer

[gmx-users] Adding a number of drugs around a polymer

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