[gmx-users] Re Multiple Chains

[Justin A. Lemkul]

C Johnson wrote:
> """
> 
> genconf -f polygly.gro -nbox 2 2 2 -o polygly_8.gro
> 
> Have you done any basic tutorial material before diving head-first into this 
> more complicated topic?
> 
> The idea is this: pdb2gmx generates the topology for the protein.  You can then 
> do whatever you choose with this definition of a protein.  After pdb2gmx, you 
> also have a coordinate file that meets force field specifications as far as 
> protonation goes.  This is the set of coordinates you should replicate, since it 
> is correct within the force field.
> """
> 
> I've done all the tutorial material hat is supplied with Gromacs...
> 
> I believe I may have got it.  These are the steps I took.
> 
> pdb2gmx -f polygly.pdb -p polygly.top -o polygly.gro
> 
> vi polygly.top
> Changed Protein count from 1 to 8
> 
> genconf -f polygly.gro -nbox 2 2 2 -o polygly_8.gro
> 
> editconf -f polygly_8 -o -d 1.0
> 
> genbox -cp out -cs -p polygly -o b4em
> 
> grompp -v -f em -c b4em -o em -p polygly
> 
> mdrun -v -s em -o em -c after_em -g emlog
> 
> grompp -f pr -o pr -c after_em -r after_em -p polygly
> 
> mdrun -v -s pr -e pr -o pr -c after_pr -g prlog >& pr.job &
> 
> grompp -v -f full -o full -c after_pr -p polygly
> 
> mdrun -v -s full -e full -o full -c after_full -g flog >& full.job &
> 
> When I look at the simulation:
> 
> ngmx -s pr -full
> 
> There are 8 short peptides.
> 
> Does anything seem wrong with these steps?
> 

If all of those steps worked, then that's a pretty good indication that you've 
got a plausible procedure.

-Justin

> Justin, thanks for the help :)
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================