[gmx-users] Error with "grompp"
Elie M
elie.moujaes at hotmail.co.uk
Wed Oct 3 16:03:47 CEST 2012
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:
"
;; 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
[ 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.
Thank you
Elie
.> Date: Tue, 2 Oct 2012 03:56:28 +0000
.> From: Emanuel.Birru at monash.edu
.> Subject: RE: [gmx-users] Error with "grompp"
> To: gmx-users at gromacs.org
>
> Hi Elie,
>
> Your email is a bit confusing but I will try to give you some idea as per my understanding of your email.
>
> If you want to use top and itp files separately, you should put all the info (molecule type, atoms, bond, pairs, angles, dihedral) in your itp files and you should use "# include "your itp file.itp" in your top file. No atom, bond, pair etc in your top file. Just like you include your water type (spc/tip4) you should include the itp. And top of that you should put the right number of molecules in the right order in your top file at the (molecules) section.
>
> Hope that might give you some help.
>
> Cheers,
> Emanuel
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Elie M
> Sent: Tuesday, 2 October 2012 1:39 PM
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] Error with "grompp"
>
>
> I am a bit confused..I am getting different errors though similar in goal. The error this time is:
> "Fatal error:Syntax error - File S54.top, line 17Last line read:'[ atoms ]'Invalid order for directive atoms"Let me tell you what I did again: I have another n2t file ( fftoplsaamod.n2t) which was used to successfully produce the .top file. Now since using grompp requires the presence of an "ffoplsaamod.itp", i just copied the original ffoplsaa.itp and renamed it and instead of it calling the two itp files :" ffoplsaanb.itp" and ""ffoplsaabon.itp", I have included these two files (in the order they should be) in the ffoplsaamod.itp file. What I am confised about is that the top file has atoms, bonds, pairs,......whilst the .itp file has atomtypes, bondtypes....why is that? what should be done to circumvent the error? shall all atomtypes in the itp be called atoms and bondtypes bonds to match that .top file or what? and which file should be in the same order of which?
>
> Thanks
> Elie
>
> > Date: Mon, 1 Oct 2012 08:38:15 -0400
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Error with "grompp"
> >
> >
> >
> > On 10/1/12 12:38 AM, Elie M wrote:
> > >
> > > Dear all,
> > > Maybe this error has been discussed before; I have checked previous messages on it but i could not resolve it. I have done a modified version of the oplsaa forcefield which I have called "ffoplsaamod.n2t". The top file was created successfully. However when I run grompp, I get the error:
> > > "Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ bondtypes ]'"
> > > I tried to "uncomment" the bond types then the error moves to contraint types. What is the solution in this case?
> > > N.B: I have copied the file ffoplsaa.itp and called it "ffoplsaamod.itp".. Not sure if this has anything to do with the error.
> >
> > It probably does. The first #include statement in your topology is probably:
> >
> > #include "ffoplsaa.itp"
> >
> > That file, in turn, calls ffoplsaanb.itp and ffoplsaabon.itp. If you
> > have renamed the files, then ffoplsaanb.itp does not occur and cannot
> > be #included prior to ffoplsaabon.itp. The order of inclusion is
> > essential for proper functionality.
> >
> > If you need to make adjustments to the contents of any of these files,
> > make a local copy of the entire force field and make modifications,
> > leaving the files located in $GMXLIB alone. Do not rename them unless
> > you consistently rename all references to these files.
> >
> > -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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