Sorry it seems that those breaks are due to hotmail and not present in the
topology. Thanks for your reply. I still have problems...I will tell u briefly
and as clear as possible what i did.
(1) My top file has the following lines ate first:
; Include forcefield parameters #include "ffoplsaamod.itp"[ moleculetype ]
which means that when grompp is reading it, it will first go to
ffoplsaamod.itp.
(2) After the description of what the ffoplsaamod is (commented by ";"), the
input is simply:
[ defaults ];nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1
3 yes 0.5 0.5
#include "ffoplsaanb.itp"#include "ffoplsaabon.itp"
where the nonbonded and bonded parameters are included in this order (which you
have also mentioned in your previous e-mail). If i run grompp in this way I get
the error:
Fatal error:Syntax error - File ffoplsaamod.itp, line 18Last line
read:'\par'Found a second defaults directive.
which I really cannot understand. The above [defaults] is the first thing that
the code will pass through. How come it mentions this as a second directory?
(3) i commented the above [ defaults] with a ";" and I get another error:
Fatal error:Syntax error - File ffoplsaanb.itp, line 1Last line read:'[
atomtypes ]'Invalid order for directive atomtypes
which might mean according to what I have read (correct me if I am wrong
please), that the order might be violated and that [atomtypes] should not come
first; but it is the first directive in the ffoplsaanb.itp file, which should
be read first.
So what might be happening? what is going wrong? or maybe what am I
missing?Thank you all once again for the effort you are making in this forum
Elie
> Date: Wed, 3 Oct 2012 10:15:07 -0400
> From: [email protected]
> To: [email protected]
> Subject: Re: [gmx-users] Error with "grompp"
>
>
>
> 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
>
> ========================================
> --
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