[gmx-users] Changed order of molecules in top

[Emma A]

Justin Lemkul <jalemkul at ...> writes:

> 
> 
> On 7/2/14, 3:31 AM, Emma Ahlstrand wrote:
> > 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?
> >
> 
> No, your coordinate file has IMI first.  grompp expects the input coordinates 
> and topology to be in the same order.  You list Zn, IMI, and SOL in the
.top - 
> that is the expected order in the coordinates.  As reported by grompp,
that is 
> not the case.  There should be no "probably" here; with such a small
system it 
> should be very easy to inspect the .gro file in a text editor and see
precisely 
> what is going on.
> 
> -Justin
> 
Hi Justin,
the problem is that my coordinate file (ZnHis2Wa2optM06.gro) has Zn first
and then two IMI and then two water and this is what I think I make with my
topology file as well, but the topology seems to produce an IMI first? 

ZnHis2Wa2
   25
    1Zn++    ZN    1   1.495   1.497   1.361
    2MOL     C1    2   1.293   1.499   1.588
    2MOL     N1    3   1.324   1.561   1.451
    2MOL     C2    4   1.166   1.556   1.632
    ...
Regards,
Emma