[gmx-users] grompp error- Excluding 3 bonded neighbours-Fatal error

[Dean Cuebas]

Dear users,
I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex

I¹ve tried to get grompp to work, but I keep getting the following message:
_______________________________________________________

>> creating statusfile for 1 node...
>> 
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
>> checking input for internal consistency...
>> calling /usr/bin/cpp...
>> processing topology...
>> Generated 165 of the 1596 non-bonded parameter combinations
>> Excluding 3 bonded neighbours for Protein             1
>> Excluding 3 bonded neighbours for IN4                 1
>> Excluding 2 bonded neighbours for SOL              8756
>> NOTE:
>>   System has non-zero total charge: 7.999998e+00
>> 
>> processing coordinates...
>> 
>> -------------------------------------------------------
>> Program grompp, VERSION 3.3.2
>> Source code file: grompp.c, line: 448
>> 
>> Fatal error:
>> number of coordinates in coordinate file (trp_b4ion.pdb, 28394)
>>              does not match topology (trp.top, 28402)
>> -------------------------------------------------------
>> 
It appears because grompp is ³excluding² the bonded neighbors is what¹s
making me end up with the different number of coordinates in my coordinate
and topology files.
Could anyone please make a suggestion how to fix this fatal error?



Below is my .mdp file that is right out of the tutorial.


Thanks so very much... I'm almost there!!!!!!!!

Dean
-- 
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas at missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897



;
;    mdp input file
;    generated by GUIMACS
;
;
; Preprocessing Parameters
;
title               =  Yo
cpp                 =  /usr/bin/cpp
define              =  -DFLEXIBLE
constraints         =  none
;
; Run Control Parameters
;
integrator          =  steep
tinit               =  0
dt                  =  0.002
nsteps              =  500
;
; Energy Minimization Parameters
;
emtol               =  1000
emstep              =  0.01
;
; Neighbor Searching Parameters
;
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
;
; Electrostatics Parameters
;
coulomb_type        =  PME
rcoulomb            =  1.0
;
; VdW Parameters
;
rvdw                =  1.4
;
; Ewald Parameters
;
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  6
ewald_rtol          =  1e-5
optimize_fft        =  yes