Hello,
It looks like you didn't load the frcmod file. Did you type, in xleap
or tleap, mods = loadamberparams frcmod_file? May I suggest you to
type the following commands:
source leaprc.gaff
mods = loadamberparams frcmod_file
loadoff lib_file.lib (or loadamberprep prep.file)
saveambperparm URE ure.prmtop ure.crd
savepdb URE ure.pdb
quit
Hope this will help
Regards
Florent Barbault
On Sun, 6 Feb 2011 09:27:09 +0400
subrata paul <paul.subrata34.gmail.com> wrote:
> Dear amber user
>
> We want to make urea molecule considering duffy model. for this
>first we
> make lib file and frcmod file.
> After loading the lib file ,we saved the molecule as pdb. then we
>want to
> save prmtop and inpcrd file from that pdb .
> u1=loadpdb ure.pdb
> saveamberparm u1 u1.prmtop u1.inpcrd
>FATAL: Atom .R <URE 1> .A<H1 1> does not have atype
>FATAL: Atom .R <URE 1> .A<H2 2> does not have atype
>FATAL: Atom .R <URE 1> .A<H3 3> does not have atype
>FATAL: Atom .R <URE 1> .A<H4 4> does not have atype
>FATAL: Atom .R <URE 1> .A<C 5> does not have atype
>FATAL: Atom .R <URE 1> .A<O 6> does not have atype
>FATAL: Atom .R <URE 1> .A<N1 7> does not have atype
>FATAL: Atom .R <URE 1> .A<N2 8> does not have atype
>Failed to generate parameters
> parameter files are not generate
>
> Why it comes as this?
> please help me
>
> thanking you
> subrata
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-------------------------------------------------
Dr Florent Barbault
Maitre de conferences / Assistant professor
Universite Paris Diderot
Laboratoire ITODYS
15 rue Jean de Baïf, bâtiment Lavoisier
75013 Paris FRANCE
http://florentbarbault.wordpress.com/
tel : (33) 01-57-27-88-50
e-mail : florent.barbault.univ-paris-diderot.fr
-------------------------------------------------
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Received on Sun Feb 06 2011 - 02:00:07 PST
