[gmx-users] Changed order of molecules in top

[Justin Lemkul]

On 7/2/14, 9:48 AM, Emma A wrote:
> 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
>      ...

Without seeing the full contents of all the files, none of this really makes 
sense.  If you can provide a link to download the full (1) topology and all 
related .itp files, (2) coordinates, and (3) .mdp files, I will take a look.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================