[gmx-users] Error message

[Mark Abraham]

Hi,

We can't tell anything from your description of your method. Obviously you
have to declare your atomtypes before you use them, so either it's not
declared, or you think it's declared but haven't organized the files
properly (e.g. included the wrong one).

Mark

On Thu, May 18, 2017 at 7:33 PM Pandya, Akash <akash.pandya.15 at ucl.ac.uk>
wrote:

> Hi,
>
> Thank you for your response. A new issue has arisen. The itp file was
> generated from SWISS PARAM. I don't understand why it can't recognise the
> NRP atomtype for Nitrogen.
>
> ERROR 1 [file GLY.itp, line 17]:
>   Atomtype NRP not found
>
> Akash
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: 18 May 2017 18:03
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error message
>
> Hi,
>
> A molecule itp does not stand in isolation.
>
> From that link "If the directive in question is atomtypes (which is the
> most common source of this error) or any other bonded or nonbonded [*types]
> directive, typically the user is adding some non-standard species (ligand,
> solvent, etc) that introduces new atom types or parameters into the system.
> As indicated above, these new types and parameters must appear before any
> [moleculetype] directive. The force field has to be fully constructed
> before any molecules can be defined."
>
> Probably you're including that .itp after some other [moleculetype].
> Declare all the atom types before any moleculetypes, like chapter 5 of the
> reference manual documents.
>
> Mark
>
> On Thu, May 18, 2017 at 6:47 PM Pandya, Akash <akash.pandya.15 at ucl.ac.uk>
> wrote:
>
> > Sorry for replying on the wrong thread. I've read the errors
> > documentation. The atomtypes directive does appear before any molecule
> > types directive in my itp file. I tried changing the order it still
> > comes up as an error
> >
> > [ atomtypes ]
> > ; name atomnum  mass    charge  ptype         sigma     epsilon
> > CR         6   12.0110   0.0        A      0.387541    0.230120
> > CO2M       6   12.0110   0.0        A      0.356359    0.292880
> > HCMM       1    1.0079   0.0        A      0.235197    0.092048
> > HNRP       1    1.0079   0.0        A      0.040001    0.192464
> > NRP        7   14.0067   0.0        A      0.329632    0.836800
> > O2CM       8   15.9994   0.0        A      0.302905    0.502080
> >
> > -----Original Message-----
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin
> > Lemkul
> > Sent: 18 May 2017 17:00
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Error message
> >
> >
> >
> > On 5/18/17 11:57 AM, Pandya, Akash wrote:
> > > Hi all,
> > >
> > > I've been trying to figure out the error message below but I'm not
> > getting anywhere. I have attached my relevant itp file. Please could
> > someone tell me what is wrong with my itp file?
> > >
> >
> > Googling the error usually turns something up...
> >
> > http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directiv
> > e_xxx
> >
> > For future reference, the list does not accept attachments.
> >
> > -Justin
> >
> > >
> > > Fatal error:
> > > Syntax error - File GLY.itp, line 7
> > > Last line read:
> > > '[ atomtypes ] '
> > > Invalid order for directive atomtypes
> > >
> > >
> > > Best regards,
> > >
> > > Akash
> > >
> > >
> > >
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
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