[gmx-users] problem in using more than one molecule of a ligand in simulation

Fri May 2 09:20:03 CEST 2014

*Dear users*

*I am evaluating interaction of a ligand with a protein named amyloid. I
want to use 5 molecules of ligand in my simulation. I run the following
commands:*

>> pdb2gmx -f bamyloid.pdb -o bamyloid.gro -p bamyloid.top -water spc

then modifying the "bamyloid.gro" and adding 5 mols of ligand.....

modifying "bamyloid.top"

>> editconf -f bamyloid.gro -o newbox.gro -bt dodecahedron -d 1.0

>> genbox -cp newbox.gro -cs spc216.gro -p bamyloid.top -o solv.gro

>> grompp -f em.mdp -c solv.gro -p bamyloid.top -o ions.tpr

this is the content of md.mdp file:

title    = Minimization

integrator   = steep

emtol    = 1000.0

emstep  = 0.01

nsteps  = 50000

energygrps  = system

nstlist  = 1

ns_type  = grid

rlist    = 1.0

coulombtype  = PME

rcoulomb   = 1.0

rvdw    = 1.0

pbc    = xyz

>> genion -s ions.tpr -o solv.ions.gro -p bamyloid.top -pname NA -nname CL
-np 40

this is the content of bamyloid.top :

 ; Include forcefield parameters

#include "gromos53a6.ff/forcefield.itp"

; Include chain topologies

#include "bamyloid_Protein_chain_A.itp"

#include "bamyloid_Protein_chain_B.itp"

#include "bamyloid_Protein_chain_C.itp"

#include "bamyloid_Protein_chain_D.itp"

#include "bamyloid_Protein_chain_E.itp"

#include "bamyloid_Protein_chain_F.itp"

#include "bamyloid_Protein_chain_G.itp"

#include "bamyloid_Protein_chain_H.itp"

#include "bamyloid_Protein_chain_I.itp"

#include "bamyloid_Protein_chain_J.itp"

#include "bamyloid_Protein_chain_K.itp"

#include "bamyloid_Protein_chain_L.itp"

#include "bamyloid_Protein_chain_M.itp"

#include "bamyloid_Protein_chain_N.itp"

#include "bamyloid_Protein_chain_O.itp"

#include "bamyloid_Protein_chain_P.itp"

#include "bamyloid_Protein_chain_Q.itp"

#include "bamyloid_Protein_chain_R.itp"

#include "bamyloid_Protein_chain_S.itp"

#include "bamyloid_Protein_chain_T.itp"

; Include ligand topology

#include "oximeo.itp"

; Include water topology

#include "gromos53a6.ff/spc.itp"

#ifdef POSRES_WATER

; Position restraint for each water oxygen

[ position_restraints ]

;  i funct       fcx        fcy        fcz

   1    1       1000       1000       1000

#endif

; Include topology for ions

#include "gromos53a6.ff/ions.itp"

[ system ]

; Name

--- in water

[ molecules ]

; Compound        #mols

Protein_chain_A     1

Protein_chain_B     1

Protein_chain_C     1

Protein_chain_D     1

Protein_chain_E     1

Protein_chain_F     1

Protein_chain_G     1

Protein_chain_H     1

Protein_chain_I     1

Protein_chain_J     1

Protein_chain_K     1

Protein_chain_L     1

Protein_chain_M     1

Protein_chain_N     1

Protein_chain_O     1

Protein_chain_P     1

Protein_chain_Q     1

Protein_chain_R     1

Protein_chain_S     1

Protein_chain_T     1

oxm                 5

SOL             17592

NA                 40

>> grompp -f em-real.mdp -c solv-ions.gro -p bamyloid.top -o em.tpr

this is the content of em-real.mdp:

title    = Minimization

integrator   = steep

emtol    = 1000.0

emstep  = 0.01

nsteps  = 50000

energygrps  =  protein oxm

nstlist  = 1

ns_type  = grid

rlist    = 1.0

coulombtype  = PME

rcoulomb   = 1.0

rvdw    = 1.0

pbc    = xyz

***** but when I run command ">> mdrun -v deffnm em", I get the following
fatal error:*

Linking all bonded interactions to atoms

There are 11265 inter charge-group exclusions,

will use an extra communication step for exclusion forces for PME

The initial number of communication pulses is: X 2

The initial domain decomposition cell size is: X 0.96 nm

The maximum allowed distance for charge groups involved in interactions is:

                 non-bonded interactions           1.000 nm

            two-body bonded interactions  (-rdd)   1.000 nm

          multi-body bonded interactions  (-rdd)   0.964 nm

Making 1D domain decomposition grid 8 x 1 x 1, home cell index 0 0 0

Initiating Steepest Descents

Charge group distribution at step 0: 2473 2348 2361 2395 2347 2304 2342 2377

Grid: 11 x 14 x 10 cells

Started Steepest Descents on node 0 Sat May  3 05:26:27 2014

Steepest Descents:

   Tolerance (Fmax)   =  1.00000e+03

   Number of steps    =        50000

           Step           Time         Lambda

              0        0.00000        0.00000

DD  step 0 load imb.: force  4.9%

-------------------------------------------------------

Program mdrun, VERSION 4.5.5

Source code file:
/home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/mdlib/pme.c, line: 538

*Fatal error:*

*80 particles communicated to PME node 6 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.*

*This usually means that your system is not well equilibrated.*

*For more information and tips for troubleshooting, please check the
GROMACS*

*website at http://www.gromacs.org/Documentation/Errors
<http://www.gromacs.org/Documentation/Errors>*

-------------------------------------------------------

*Could anyone tell me how to solve this problem???*

*your help is appreciated....*

-- 
*********************
Dr. Hamid Irannejad (Pharm D. & PhD)
Department of Medicinal Chemistry
Faculty of Pharmacy
Mazandaran University of Medical Sciences
Sari, Iran
Fax: 0098 151 3543084
Postal code: 4847116547
http://orcid.org/0000-0001-7513-6162
*************************