Please check your coordinate file. There seems to be something wrong with the structure.
And there is some parameter missing, please look at your input coordinate carefully.
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Manjula Saravanan [mailto:manjusimba.gmail.com]
Sent: Wednesday, January 18, 2017 4:23 PM
To: amber.ambermd.org
Subject: [AMBER] Error while creation topology and coordinate files in tleap
Dear Sir,
We are trying to create topology and coordinate files in tleap.
We are getting the following error after running the saveamberparm command.
The error statement goes like this,
saveamberparm COMPLEX solv.prmtop solv.inpcrd Checking Unit.
WARNING: There is a bond of 10.545950 angstroms between:
------- .R<EST 631>.A<C15 16> and .R<EST 631>.A<C17 18>
WARNING: There is a bond of 6.708769 angstroms between:
------- .R<EST 631>.A<C11 12> and .R<EST 631>.A<C13 14>
WARNING: There is a bond of 4.697628 angstroms between:
------- .R<EST 631>.A<C6 7> and .R<EST 631>.A<C8 9>
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: c3 - oh - c2 Building proper torsion parameters.
1-4: angle 3989 4003 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3985 4003 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3985 3986 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3985 3989 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3985 3990 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3985 3995 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3985 4003 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3985 3986 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3985 3989 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3985 3990 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3985 3995 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3985 4003 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3985 3989 duplicates bond ('triangular' bond) or angle ('square'
bond)
Building improper torsion parameters.
total 749 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
Due to this error we cant create the input files for MD. Kindly help us in this regard.
*With Best Regards*
*S. Manjula*
*Research Scholar*
*Laboratory of Biocrystallography and Computational Molecular Biology* *Department of Physics* *Periyar University*
*Salem-11*
*Tamilnadu*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 18 2017 - 03:30:03 PST
