[gmx-users] GRO File Merging

[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
<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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