sunny mishra wrote:
Hi All,
I am running simulation of a system containing Coarse Grained 1SU4
(Minimized structure) and Coarse Grained DPPC lipid. I used the
INFLATEGRO script to inflate the lipid and removed the overlapping
lipids with proteins and then running the energy minimization.
grommp says there are mismatching of atoms in system.top file (which
consists of DPPC, Protein and W) and inflated_bilayer.gro (Which
Inflategro script developed). I don't know why this is happening and why
the atoms are not matching. Also, is there any problem with the
atom2cg.awk script which MARTINI guys provided or they have any other
script which converts the atomic structure of protein to CG protein so
that at the time of simulation the atoms match.
I am using the grompp command something like this.
grompp -f em.mdp -c inflated_bilayer.gro -p system.top -maxwarn 10
grompp says: atom name 1 in system.top and inflated_bilayer.gro does not
match (NC3-BCQd)
This is normal. Please see the MARTINI documentation - it explicitly describes
what each script, etc. is doing - the initial CG structure contains generic atom
names, which are replaced in this step.
As a note, this is pretty much the *only* situation where mismatches are useful
or appropriate. Most of the time (as we have seen recently), mismatches lead to
catastrophic problems later :)
-Justin
and it keeps on going until 2116 atoms.
I dnt know how to fix this. Reply will be appreciable.
Thanks,
Sunny
--
========================================
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
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