[gmx-users] GRO File Merging

[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 <sanimr at mail.usf.edu> 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
> <https://www.linkedin.com/pub/sanim-rahman/108/a64/986>
>
>
> On Sat, Feb 25, 2017 at 2:59 PM, Mark Abraham <mark.j.abraham at gmail.com>
> 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 <sanimr at mail.usf.edu> 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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