[gmx-users] No such moleculetype Na

[Tsjerk Wassenaar]

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