[gmx-users] KALP-15 in DPPC tutorial

[Justin Lemkul]

On 3/16/15 12:08 AM, BAOLIN HUANG wrote:
> Hi All, I am doing the GROMACS Tutorial of KALP-15 in DPPC. Now, I get stuck
> at "Note how many lipids were deleted and update the [ molecules ] directive
> of your topology accordingly. Run energy minimization. Then, scale down the
> lipids by a factor of 0.95 (assuming you have used default names, the result
> of the minimization is called "confout.gro"): perl inflategro.pl confout.gro
> 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat"
>
> The command line was gmx grompp -f minim.mdp -c system_inflated.gro -p
> topol.top -o em.tpr. And I got Fatal error: number of coordinates in
> coordinate file (system_inflated.gro, 6438) does not match topology
> (topol.top 888444) I tried to add DPPC 128 in the [ molecules ], however, I

You should never, at any point, have 888444 atoms in the system.  Likely you've 
added water to the inflated system.  Don't.

> got Fatal error: No such moleculetype DPPC.
>
> How to update the [molecules] in topol.top? And how do I know the number of
> molecules?
>

You start with 128, InflateGRO prints out how many it removes...then use a text 
editor.

-Justin

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

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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