[gmx-users] problem with Charmm36 ff

Esteban.Pedrueza at uv.es Esteban.Pedrueza at uv.es
Wed Jun 18 16:25:34 CEST 2014

Dear gmx users,
I am trying to make MD for a DPPC bilayer with a melittin protein (pbd 
ID: 2MLT) positioned in the water slab, using Charmm36 ff for the lipids 
and Charmm22 for melittin, following this paper (Andersson, et all 
Biophysical Journal Volume 104 March 2013 L12–L14).  The procedure is 
the following:
1) I go to Klauda web page 
(http://terpconnect.umd.edu/~jbklauda/research/download.html) and 
download the DPPC bilayer (pdb file), eliminate the water and make: 
pdb2gmx -f bilayer.pdb -o bilayer.gro (choosing CHARMM36 all-atom force 
field, previously downloaded from charmm36-mar2014.ff from Charmm 
webpage, and tip3p water)

2)for the melittin: pdb2gmx -f 2MLT.pdb -o 2MLT.gro (choosing  CHARMM27 
all-atom force field (with CMAP) - version 2.0,  and tip3p water)

I merged the 2 .gro's and solvated and it is OK. However, when I go to 
add ions with grompp, I obtain the following error:

Program grompp, VERSION 4.6.5
Source code file: /home/pedrueza/gromacs-4.6.5/src/kernel/toppush.c, 
line: 1336

Fatal error:
Atomtype HB not found
For more information and tips for troubleshooting, please check the 
website at http://www.gromacs.org/Documentation/Errors

My topol.top file is this: (previously I modified the topol.top files to 
itp simply erasing the #include "charmm27.ff/forcefield.itp" (2MLT) and 
#include "charmm36-mar2014.ff/forcefield.itp" (dppc), besides the 
[molecules], [system] and the other directives, like posre or ions .itp)

; Include forcefield parameters
#include "charmm36-mar2014.ff/forcefield.itp"

; Include chain topologies
#include "dppc.itp"
#include "2MLT.itp"

; Include water topology
#include "charmm36-mar2014.ff/tip3p.itp"

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

; Include Position restraint file
#ifdef POSRES
#include "posre_dppc.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre_2MLT.itp"

; Include topology for ions
#include "charmm36-mar2014.ff/ions.itp"

[ system ]
; Name
DPPC bilayer plus 2MLT in water

[ molecules ]
; Compound        #mols
Other               72	
Protein             1
SOL              4054

I think is a problem with nomenclature of atoms, but it is strange the 
mixing of the 2 forcefields???
I am new in GMX so any help is highly appreciated. If you need I can 
provide the rest of files 
Esteban Pedrueza Villalmanzo
esteban.pedrueza at uv.es
espevi1982 at hotmail.com

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