[gmx-users] No such moleculetype Na

[swatik at ncbs.res.in]

Hi Tsjerk,
 Thanks for your suggestion.I tried to change the ions.itp as follows :

#ifdef _FF_AMBER03

[ moleculetype ]
; molname       nrexcl
Na+             1

[ atoms ]
; id    at type res nr  residu name     at name  cg nr  charge
1       Na      1       Na              Na       1      1

#endif

But still I am getting same problem.Kindly advice.

Regards,
Swati


> Hi Swati,
>
> Sorry, I wasn't  paying that much attention indeed and failed to
> notice you were dealing with Amber. There's nothing wrong with your
> installation in this regard; Gromacs just does not have Amber included
> by default. I'm not sure if there's an ions.itp for Amber somewhere,
> but it's not too hard writing the moleculetype 'Na' yourself. Just
> take one of the ones in ions.itp and set the names and atom type
> accordingly.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Apr 22, 2009 at 10:14 AM,  <swatik at ncbs.res.in> wrote:
>> Hi Tsjerk,
>> Thanks for your reply. ions.itp is already included in topology file.
>> However after you mentioned I checked the ions.itp file. But I think it
>> defines molecule type only for gromacs force fields and the OPLS force
>> field. The headers are only these three
>> #ifdef _FF_GROMACS
>> #ifdef _FF_GROMOS96
>> #ifdef _FF_OPLS
>> Is this a problem with my GROMACS installation? Kindly advice.
>> Thanks.
>> Swati
>>
>>
>>> Hi Swati,
>>>
>>>> Fatal error:
>>>> No such moleculetype Na
>>>>
>>>> But the atom type is present in ffamber03.rtp. I tried changing the
>>>> atom
>>>> name to NA and Na+. But I still get similar error. Kindly help.
>>>
>>> It doesn't complain about the atom type, but about the moleculetype.
>>> Did you #include "ions.itp"? That file contains the moleculetype
>>> definitions for a series of ions, including Na/NA/NA+. The naming
>>> depends on the force field.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>> Junior UD (post-doc)
>>> Biomolecular NMR, Bijvoet Center
>>> Utrecht University
>>> Padualaan 8
>>> 3584 CH Utrecht
>>> The Netherlands
>>> P: +31-30-2539931
>>> F: +31-30-2537623
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>>
>>
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
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