Dear Anju,
Did you choose the atom types yourself or did antechamber select these?
If you chose them yourself then your choices are inapropriate. For example
leap is telling you that it has no parameters for oh-h1 which would be
"Oxygen in hydroxyl group" bound to "H bonded to aliphatic carbon with 1
electrwd. group" which is clearly wrong since and oxygen is not an aliphatic
carbon. The more appropriate choice would be ho = "Hydroxyl group".
If you don't have a lot of experience with molecular mechanics simulations
and parameter determination I would suggest that you don't try to select the
parameters yourself but instead let antechamber do it for you and then
carefully review what antechamber gives you - particularly with regards to
parameters it gives you in a frcmod file when you run parmchk.
If, however, you used antechamber to obtain the atom types then there is
clearly a problem in antechamber that we need to investigate.
All the best
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 <
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: Wednesday, August 01, 2007 22:25
To: amber.scripps.edu
Subject: Re: AMBER: Problem while saving .top and .crd files.
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 <
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 - 06:07:28 PDT
