Hello Sir,
As directed i carried out changes in my Pdb fileof the drug molecule, force
field used is leaprc.gaff, and types that i have used are (as given in
leaprc.gaff):
C: sp2 hybridization = c
C: sp3 hybridization = c3
H: sp3 hybridization = h1
O: sp3 hybridization = oh
N: sp3 hybridization = n3
Now again while trying to save .top and .crd files following errror appears:
-------------------------------------------------------------------------------------------------------
Could not find bond parameter for : oh - h1
Could not find bond parameter for : c - h1
Could not find bond parameter for : c - n3
Could not find bond parameter for : n3 - h1
-
-
Building angle parameters.
Could not find angle parameter for: c - c - h1
Could not find angle parameter for: c - oh - h1
Could not find angle parameter for: h1 - c - c
Could not find angle parameter for: c - c - n3
Could not find angle parameter for: c - n3 - c3
Could not find angle parameter for: h1 - n3 - c3
-
-
-
-
Could not find angle parameter for: c3 - oh - h1
Building proper torsion parameters.
** No torsion terms for c-c-n3-h1
** No torsion terms for c-c-n3-c3
** No torsion terms for c-c-n3-h1
** No torsion terms for h1-n3-c-c
** No torsion terms for c3-n3-c-c
** No torsion terms for c-c-n3-h1
** No torsion terms for c-c-n3-c3
Building improper torsion parameters.
total 0 improper torsion applied.
Building H-Bond parameters.
Parameter file was not saved.
------------------------------------------------------------------------------------------------------------
On 7/31/07, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> Hi Anju,
>
> You need to provide parameters for any bonds, angles and dihedrals that
> you have in your system that are not in the standard force fields. Where did
> you get the atom types for your drug molecule? If you are using analogy to
> the underlying amino acid force field then you need to calculate any missing
> parameters. If you are new to AMBER without experience of force field
> derivation then I suggest you stick to antechamber for you drug molecule and
> only once you are completely familiar with things you attempt to determine
> your own atom types and ultimately parameters.
>
> See http://amber.scripps.edu/tutorials/basic/tutorial4/index.htm for a
> tutorial on antechamber.
>
> >How to overcome dis error nd save d topology and coordinate file?
>
> And please try to avoid text message grammar in email messages when you
> have a real keyboard to type on.
>
> Good luck...
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> ------------------------------
> *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *Anju Sharma
> *Sent:* Monday, July 30, 2007 20:48
> *To:* amber.scripps.edu
> *Subject:* AMBER: Problem while saving .top and .crd files.
>
>
> Hello Amber users,
>
> While trying to save .top and .crd files for my drug molecule in xleap i
> encounterd following error:
>
> --------------------------------------------------------------------------------------------------------------
> Could not find angle parameter (ex: H-C-C, there are lot more lk dis)
> Could not find bond parameter (ex: OH-H, and many more)
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 4 improper torsions applied.
> Building H-bond parameters.
> Parameter file was not saved.
>
> -------------------------------------------------------------------------------------------------------------
> How to overcome dis error nd save d topology and coordinate file?
>
> Regards,
> --
> Anju Sharma
> Project Fellow,
> NIT, Hamirpur (H.P.)
>
>
--
Anju Sharma
Project Fellow,
NIT, Hamirpur (H.P.)
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Received on Sun Aug 05 2007 - 06:07:19 PDT
