[gmx-users] POPC simulation

Venky Krishna venky.agas at gmail.com
Thu Jun 1 02:25:13 CEST 2006

Hi all,

I had similar problem with Fatal errors with Atomtype LC3 not found  
while setting up a POPC simulation. After a day of trying out  
different things I figured out the problem. And I would like to share  
my experience in the mailing list.

Renaming of POP to POPC in the .gro files doesn't matter... the main  
thing is to change the [Defaults] in the lipid.itp file (this  
eliminates the LC3 atomtype not found error)
my .top files and modified lipid.itp files look like.


#include "ffgmx.itp"
#include "lipid.itp"
#include "popc.itp"
#include "protein.top"
#include "spin.top"
#include "ions.itp"

#ifdef FLEX_SPC	; removed these following lines from the protein.top  
file and appended into one single .top file.
#include "flexspc.itp"
#include "spc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
    1    1       1000       1000       1000

[ system ]
; name

[ molecules ]
; name	number
Protein 	1
DRG		1
POPC		154
SOL     	13393
lipid.itp (notice the defaults directive is commented out... this  
eliminates the AtomType 'LC3' not found error)

;; this forcefield is a mixture of lipid and GROMOS parameters. GROMOS
;; parameters taken from ffgmxnb.itp, lipid parameters from Berger et
;; al, Biophys. J. 72, pp. 2002-2013. Parameters starting with L are
;; lipid parameter. LP2 and LP3 are Bergers pentadecane parameters,
;; the rest is OPLS. The lipids see SPC/SPCE, and lipids as
;; OPLS/Berger, protein as GROMOS, the protein sees lipids as GROMOS.

;[ defaults ]
;1       1

[ atomtypes ]
;name     mass     charge ptype  c6           c12
    LO    15.9994    0.000  A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS
   LOM    15.9994    0.000  A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS
   LNL    14.0067    0.000  A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS
    LC    12.0110    0.000  A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS
   LH1    13.0190    0.000  A 4.03100e-03 1.21400e-05 ;CH1, OPLS
   LH2    14.0270    0.000  A 7.00200e-03 2.48300e-05 ;CH2, OPLS
    LP    30.9738    0.000  A 9.16000e-03 2.50700e-05 ;phosphor, OPLS
   LOS    15.9994    0.000  A 2.56300e-03 1.86800e-06 ;ester oxygen,  
   LP2    14.0270    0.000  A 5.87400e-03 2.26500e-05 ;RB CH2,  
Bergers LJ
   LP3    15.0350    0.000  A 8.77700e-03 3.38500e-05 ;RB CH3,  
Bergers LJ
   LC3    15.0350    0.000  A 9.35700e-03 3.60900e-05 ;CH3, OPLS
   LC2    14.0270    0.000  A 5.94700e-03 1.79000e-05 ;CH2, OPLS



That is all the modifications required for running the simulation.  
Hope this helps people with similar problem in the future.


Venky Krishnamani
Dr.Janos K. Lanyi Lab,
D320, Medical Sciences D
University of California, Irvine

On May 29, 2006, at 12:23 PM, Arindam Ganguly wrote:

> Hi All,
> thanks to Steffan , Jim and Kaushal for helping me out in the POPC  
> simulation setup. i finally got everything to work. i guess the imp  
> thing was to change the POPC to POP in .top file. thanks once again.
> Arindam Ganguly
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