It looks as Leap worked properly now ...
vlad
john chen wrote:
> Dear amber experts,
>
> Having asked about atom types, I subsequently realised that atoms NP,
> NO and CX are
> defined in parm94.dat but not in parm99.dat...
>
> all I did was change in parm99.dat the original:
>
> HW OW 0000. 0000. 4. flag for
> fast water
>
> N NA N2 N* NC NB NT NY
> C* CA CB CC CD CK CM CN CQ CR CV CW CY CZ
>
> MOD4 RE
>
> to this:
>
> HW OW 0000. 0000. 4. flag for
> fast water
>
> N NA N2 N* NC NB NT NY NP NO
> C* CA CB CC CD CK CM CN CQ CR CV CW CX CY CZ
>
> MOD4 RE
>
> On rerunning the script, at the saveamberparm command, I now get the
> output below.
> Are the topology files and coordinate files OK now, or is there
> something else that I have to change
> in parm99.dat?
>
> I appologise for the last email.
>
> with best regards,
> JC.
>
>
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> old PREP-specified impropers:
> <HEM 89>: NA C1A C4A FE
> <HEM 89>: NB C1B C4B FE
> <HEM 89>: NC C1C C4C FE
> <HEM 89>: ND C1D C4D FE
> <HEM 89>: C1A C2A NA CHA
> <HEM 89>: C1B C2B NB CHB
> <HEM 89>: C1C C2C NC CHC
> <HEM 89>: C1D C2D ND CHD
> <HEM 89>: C2A C3A C1A CAA
> <HEM 89>: C2B C3B C1B CMB
> <HEM 89>: C2C C3C C1C CMC
> <HEM 89>: C2D C3D C1D CMD
> <HEM 89>: C3A C4A C2A CMA
> <HEM 89>: C3B C4B C2B CAB
> <HEM 89>: C3C C4C C2C CAC
> <HEM 89>: C3D C4D C2D CAD
> <HEM 89>: C4A NA C3A CHB
> <HEM 89>: C4B NB C3B CHC
> <HEM 89>: C4C NC C3C CHD
> <HEM 89>: C4D ND C3D CHA
> total 364 improper torsions applied
> 20 improper torsions in old prep form
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> CALA 1
> NALA 1
>
--
----------------------------------------------------------------------------
Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
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Received on Wed Sep 12 2007 - 06:07:45 PDT
