[gmx-users] Error with "grompp"

[Justin Lemkul]

On 10/3/12 10:03 AM, Elie M wrote:
>
> Hello Emanuel.
> First of all thank you for your help. I am sorry if my previous e-mail was a bit confusing.  I will tell what I did recently.
> (1) I removed all the information :molecule type, atoms, bond....dihedral from my top file and pasted them to the ipt file , the one I called ffoplsaamod.itp; I also included an "#include command# referring to the .itp file. so my top file now just looks like that:
> "

That doesn't really make any sense.  You've chopped out the information for your 
molecule from the topology that g_x2top wrote, then simply re-included that 
information?  The output of g_x2top should be a functional topology; you should 
not have to adjust it.  If you need this topology to be an .itp file, i.e. as a 
ligand in some other .top, then you only need to make small adjustments.  See 
the following:

http://www.gromacs.org/Documentation/File_Formats/.itp_File

> ;;	File 'S54.top' was generated;	By user: User (1000);	On host: User-PC;	At date: Wed Sep 26 01:43:14 2012;;	This is your include topology file;	Generated by x2top;#include "ffoplsaamod.itp"  "
> and my foplsaamod.itp has the info that was present in .top file i.e:
> "[ moleculetype ]
>
> ; Name            nrexcl
>
> S54NS               3
>
>
>
> [ atoms ]
>
> ;   nr
> type  resnr residue  atom
> cgnr     charge       mass
> typeB    chargeB      massB
>
>       1
> opls_145      1    LIG
> C      1          0
> 12.011   ; qtot 0
>
>       2
> opls_735      1    LIG
> C      2          0
> 12.011   ; qtot 0
>
>       3
> opls_734      1    LIG
> S      3          0
> 32.06   ; qtot 0
>
>       4
> opls_735      1    LIG
> C      4          0
> 12.011   ; qtot 0
>
>       5
> opls_145      1
> LIG      C      5
> 0     12.011   ; qtot 0
>
>       6
> opls_145      1    LIG
> C      6          0
> 12.011   ; qtot 0
>
>       7
> opls_516      1    LIG
> C      7          0
> 12.011   ; qtot 0
>
>       8
> opls_516      1    LIG
> C      8          0
> 12.011   ; qtot 0....[ bonds ]...37    36
> 42    83     1
>
>     35
> 37    38    39
> 1
>
>     37
> 38    39    40
> 1
>
>     38
> 39    40    36
> 1
>
>     36
> 40    46    92
> 1
>

I don't know whether it is your email client or the topology itself, but the 
seemingly random line breaks make these posts very difficult to read.

>
>
> [ system ]
>
> ; Name
>
> S54NS
>
>
>
> [ molecules ]
>
> ; Compound        #mols
>
> S54NS               1
>
>   "Have I missed something? i guess I did. I am getting an error of the form (when executing grompp_:
> Invalid order for directive [atoms].
> (2) What about the ffoplsaabon.itp and ffoplsaanb.itp files? Do they have to be put somewhere.
> I am sorry to bombard u with all of this but I have got my head spinning thinking about topologies and fixing this error.
>

A topology follows a defined structure that must be observed.  The hierarchy is 
described in the manual, but can be distilled into the following requirements:

1. You must #include a force field that defines all default elements (i.e. a 
[defaults] directive) that govern how the force field operates.

2. You must #include the nonbonded and bonded parameters for that force field, 
in that order.  Bonded parameters are assigned based on atom types, which must 
be declared first in order to be used.

3. After all force field-level parameters (items 1 and 2), you can introduce 
molecules that use these parameters.  This is the point where you can proceed to 
[atoms], [bonds], etc for a particular molecule.

-Justin

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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