Re: [gmx-users] GRO File Merging

2017-02-26 Thread Justin Lemkul 



On 2/26/17 10:54 AM, Justin Lemkul wrote:



On 2/25/17 3:10 PM, 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.



Nitpick: there's no such thing as a CHARMM27 protein force field.  What you're
using is CHARMM22/CMAP with various revisions that were made to it prior to
CHARMM36 in 2012.  CHARMM27 refers exclusively to the CHARMM nucleic acid force
field released in 2000 (which was superseded by the CHARMM36 nucleic acid force


...and the C27 lipids that were included in the force field, of course.  But 
there's no "CHARMM27 protein force field," though you often see that misnomer in 
the literature.


-Justin


field in 2011, and is much better).

-Justin


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
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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 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] GRO File Merging

2017-02-26 Thread Justin Lemkul 



On 2/25/17 3:10 PM, 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.



Nitpick: there's no such thing as a CHARMM27 protein force field.  What you're 
using is CHARMM22/CMAP with various revisions that were made to it prior to 
CHARMM36 in 2012.  CHARMM27 refers exclusively to the CHARMM nucleic acid force 
field released in 2000 (which was superseded by the CHARMM36 nucleic acid force 
field in 2011, and is much better).


-Justin


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
--
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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 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] 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!
> > >
> > > * 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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> > * Please search the archive at http://www.gromacs.org/
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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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
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> * Please search the archive at http://www.gromacs.org/
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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
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> 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

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