AMBER Archive (2007)

Subject: AMBER: FATAL: Atom .R<CYF 17>.A<N 1> does not have a type.

From: Boutheina Kerkeni (b.kerkeni_at_ucl.ac.uk)
Date: Wed Dec 05 2007 - 17:28:41 CST

Dear Dr CAse
Thanks very much for the files.
1)I managed to have some parameters for all my non standard residues
in my pdb file. And created new unit names for modifed CYS and HIS.
But my respective lib files do not contain any H atom- compared to
the CYF.off that you sent me (exple: HN, HA, HB3,HB2...) How did you
include these to the .lib?
In my case I did this:
CYF=loadpdb cyf.pdb
edit CYF
and used draw bond command in xleap then
I edited the selection, entered charges, then save and quit table
then
saveoff CYF cyf.lib

2) I have raised this issue, because, when I load off all my lib
files obtained as I described above, and loaded the frcmod files to
xleap , the loaded my PDB file
defined all necessary bonds usin the bond command
then solvateOct
added ions to neutralize all went fine until, I wanted to save prmtop
and inpcrd
xleap complains about FATAL .... does not have a type
Any suggestions to overcome this are very welcome?
Thanks in advance
Regards
> FATAL: Atom .R<CYF 17>.A<N 1> does not have a type.
> FATAL: Atom .R<CYF 17>.A<CA 2> does not have a type.
> FATAL: Atom .R<CYF 17>.A<C 3> does not have a type.
> FATAL: Atom .R<CYF 17>.A<O 4> does not have a type.
> FATAL: Atom .R<CYF 17>.A<CB 5> does not have a type.
> FATAL: Atom .R<CYF 17>.A<SG 6> does not have a type.
> FATAL: Atom .R<CYF 20>.A<N 1> does not have a type.
> FATAL: Atom .R<CYF 20>.A<CA 2> does not have a type.
> FATAL: Atom .R<CYF 20>.A<C 3> does not have a type.
> FATAL: Atom .R<CYF 20>.A<O 4> does not have a type.
> FATAL: Atom .R<CYF 20>.A<CB 5> does not have a type.
> FATAL: Atom .R<CYF 20>.A<SG 6> does not have a type.
> FATAL: Atom .R<CYF 112>.A<N 1> does not have a type.
> FATAL: Atom .R<CYF 112>.A<CA 2> does not have a type.
> FATAL: Atom .R<CYF 112>.A<C 3> does not have a type.
> FATAL: Atom .R<CYF 112>.A<O 4> does not have a type.
> FATAL: Atom .R<CYF 112>.A<CB 5> does not have a type.
> FATAL: Atom .R<CYF 112>.A<SG 6> does not have a type.
> FATAL: Atom .R<CYF 148>.A<N 1> does not have a type.
> FATAL: Atom .R<CYF 148>.A<CA 2> does not have a type.
> FATAL: Atom .R<CYF 148>.A<C 3> does not have a type.
> FATAL: Atom .R<CYF 148>.A<O 4> does not have a type.
> FATAL: Atom .R<CYF 148>.A<CB 5> does not have a type.
> FATAL: Atom .R<CYF 148>.A<SG 6> does not have a type.
> FATAL: Atom .R<HIF 185>.A<N 1> does not have a type.
> FATAL: Atom .R<HIF 185>.A<CA 2> does not have a type.
> FATAL: Atom .R<HIF 185>.A<C 3> does not have a type.
> FATAL: Atom .R<HIF 185>.A<O 4> does not have a type.
> FATAL: Atom .R<HIF 185>.A<CB 5> does not have a type.
> FATAL: Atom .R<HIF 185>.A<CG 6> does not have a type.
> FATAL: Atom .R<HIF 185>.A<ND1 7> does not have a type.
> FATAL: Atom .R<HIF 185>.A<CD2 8> does not have a type.
> FATAL: Atom .R<HIF 185>.A<CE1 9> does not have a type.
> FATAL: Atom .R<HIF 185>.A<NE2 10> does not have a type.
>

On 4 Dec 2007, at 18:57, David A. Case wrote:

> On Wed, Nov 28, 2007, Boutheïna Kerkeni wrote:
>>
>>
>> Would you please send me any parameters of your Fe4S4? Did you also
>> parameterize Fe3S4?
>
> Cubane files are in the attached tar file. We have not looked yet
> at Fe3S4.
>
> ...regards...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | skype: dacase
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================<fe4
> s4.tar>

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