[gmx-users] coordinate error

Maximiliano Figueroa Yévenes maxfigue at udec.cl
Mon Sep 6 17:09:40 CEST 2004


Hi, I am simulated a big system: 48 chains, with 572394 atoms (8100 aa + 
148162 waters) in OPLS/AA forcefield. But I have a problem, when I use the 
"grompp" this send me this error:

processing coordinates...
Fatal error: number of coordinates in coordinate file (b4em.gro, 572394)
             does not match topology (antena.top, 572119)

But I check the coordinate file, and this has 572394... check the antena.top, 
and this has only the 48 chains, check this 48 chains, sum the coordinates, 
and this more waters are 572394!!! no 572119. What is wrong? my system is too 
big?

Attached top file

;
;	File 'antena.top' was generated
;	By user: maxi (501)
;	On host: alfa
;	At date: Sat Sep  4 21:04:17 2004
;
;	This is your topology file
;	? 
;
; Include forcefield parameters
#include "ffoplsaa.itp"

; Include chain topologies
#include "antena_a.itp"
#include "antena_b.itp"
#include "antena_c.itp"
#include "antena_d.itp"
#include "antena_e.itp"
#include "antena_f.itp"
#include "antena_g.itp"
#include "antena_h.itp"
#include "antena_i.itp"
#include "antena_j.itp"
#include "antena_k.itp"
#include "antena_l.itp"
#include "antena_m.itp"
#include "antena_n.itp"
#include "antena_o.itp"
#include "antena_p.itp"
#include "antena_q.itp"
#include "antena_r.itp"
#include "antena_s.itp"
#include "antena_t.itp"
#include "antena_u.itp"
#include "antena_v.itp"
#include "antena_w.itp"
#include "antena_x.itp"
#include "antena_y.itp"
#include "antena_z.itp"
#include "antena_A.itp"
#include "antena_B.itp"
#include "antena_C.itp"
#include "antena_D.itp"
#include "antena_E.itp"
#include "antena_F.itp"
#include "antena_G.itp"
#include "antena_H.itp"
#include "antena_I.itp"
#include "antena_J.itp"
#include "antena_K.itp"
#include "antena_L.itp"
#include "antena_M.itp"
#include "antena_N.itp"
#include "antena_O.itp"
#include "antena_P.itp"
#include "antena_Q.itp"
#include "antena_R.itp"
#include "antena_S.itp"
#include "antena_T.itp"
#include "antena_U.itp"
#include "antena_V.itp"

; Include water topology
#include "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 generic topology for ions
#include "ions.itp"

[ system ]
; Name
?  in water

[ molecules ]
; Compound        #mols
Protein_a           1
Protein_b           1
Protein_c           1
Protein_d           1
Protein_e           1
Protein_f            1
Protein_g           1
Protein_h           1
Protein_i            1
Protein_j            1
Protein_k           1
Protein_l            1
Protein_m          1
Protein_n           1
Protein_o           1
Protein_p           1
Protein_q           1
Protein_r            1
Protein_s           1
Protein_t            1
Protein_u           1
Protein_v           1
Protein_w          1
Protein_x           1
Protein_y           1
Protein_z           1
Protein_A           1
Protein_B           1
Protein_C           1
Protein_D           1
Protein_E           1
Protein_F            1
Protein_G           1
Protein_H           1
Protein_I            1
Protein_J           1
Protein_K           1
Protein_L           1
Protein_M           1
Protein_N           1
Protein_O           1
Protein_P           1
Protein_Q           1
Protein_R           1
Protein_S           1
Protein_T           1
Protein_U           1
Protein_V           1
SOL             148162
 

HElP ME!!! I need simulated for 200 ps

Thanks



More information about the gromacs.org_gmx-users mailing list