[gmx-users] Changed order of molecules in top

[Emma Ahlstrand]

Hi,

I have a problem with that the order of atoms in my topology does not match the order of atoms in the gro-file. I use amber99sb and I have built itp-files on my own for the molecules that are not present in the "library". Each IMI contains 9 atoms and each SOL 3 atoms and the ZN is one atom so in total it should be 9*2+3*2+1=25 atoms in total, which is present in the .gro file, but when I run with the topology-file pasted below I get a error the this file contains 34 atoms.

This is my topologyfile:

; Include forcefield parameters
#include "amber99sb.ff/forcefield.itp"


; Additional atom types

[ atomtypes ]
; name at_name at_num mass     charge   ptype  sigma        epsilon     ; sw   ref
Zn++  Zn++    30     65.37000  2.000    A    1.94216e-01  1.046       ; 1    Stote Proteins 23:12 1995

; Include topology for ions
#include "zn.itp"

; Include water topology
#include "spcetestamber.itp"

; Include topology for imidazole
#include "imiamberrtp.itp"

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

[system ]
; Name
ZnHis2Wa2

[ molecules ]
; Compound        #mols
ZN2+             1
IMI              2
SOL              2

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

Fatal error:
number of coordinates in coordinate file (ZnHis2Wa2optM06.gro, 25)
             does not match topology (ZnHis2Wa2optM06amber.top, 34)


Since the difference is 9 atoms, I thought that the difference is one IMI, so I tried with one less IMI in the topology, printed below.

; Include forcefield parameters
#include "amber99sb.ff/forcefield.itp"


; Additional atom types

[ atomtypes ]
; name at_name at_num mass     charge   ptype  sigma        epsilon     ; sw   ref
Zn++  Zn++    30     65.37000  2.000    A    1.94216e-01  1.046       ; 1    Stote Proteins 23:12 1995

; Include topology for ions
#include "zn.itp"

; Include water topology
#include "spcetestamber.itp"

; Include topology for imidazole
#include "imiamberrtp.itp"

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

[system ]
; Name
ZnHis2Wa2

[ molecules ]
; Compound        #mols
ZN2+             1
IMI              1
SOL              2


Then the number of atoms matches, but I get the information that the atom names does not match.

Warning: atom name 1 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro does not match (C1 - ZN)
Warning: atom name 2 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro does not match (N1 - C1)

By this message it gets clear to me that the topology makes an IMI first and then go on to the ZN and then probably the IMI and the two waters specified in the top-file. Why does it do that? And how do I correct it?

Thanks in advance for help.


------------------------------
Emma Ahlstrand
PhD student

Linnaeus University
Faculty of Health and Life Sciences
391 82 Kalmar / 351 95 Växjö

+46 480 446 152 Telephone
+46 73 905 7186 Mobile
emma.ahlstrand at lnu.se
http://lnu.se/ccbg