[gmx-users] Error message

[Pandya, Akash]

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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