I give up - you do not seem to understand anything I write.
Bill
On 7/11/17 2:52 PM, Rana Rehan Khalid wrote:
> Dear Sir I actually read some previous threads about similar kind of
> problem in which (some one suggested that we can ignore these thats why i
> asked i saw the advice on the end of output) so when i tried to prepared
> the parmtop and crd file then this output shows. and files created.
> Checking Unit.
> WARNING: There is a bond of 64.665185 angstroms between:
> ------- .R<HEO 187>.A<FO 1> and .R<HEO 187>.A<NA 2>
> WARNING: There is a bond of 63.582771 angstroms between:
> ------- .R<HEO 187>.A<FO 1> and .R<HEO 187>.A<O1 74>
> WARNING: There is a bond of 62.142422 angstroms between:
> ------- .R<HEO 187>.A<FO 1> and .R<HEO 187>.A<NB 23>
> WARNING: There is a bond of 60.983924 angstroms between:
> ------- .R<HEO 187>.A<FO 1> and .R<HEO 187>.A<NC 39>
> WARNING: There is a bond of 63.580412 angstroms between:
> ------- .R<HEO 187>.A<FO 1> and .R<HEO 187>.A<ND 55>
> WARNING: The unperturbed charge of the unit: -12.000000 is not zero.
>
> -- ignoring the warnings.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> old PREP-specified impropers:
> <HEO 187>: NA C1A C4A FO
> <HEO 187>: NB C1B C4B FO
> <HEO 187>: NC C1C C4C FO
> <HEO 187>: ND C1D C4D FO
> <HEO 187>: C1A C2A NA CHA
> <HEO 187>: C1B C2B NB CHB
> <HEO 187>: C1C C2C NC CHC
> <HEO 187>: C1D C2D ND CHD
> <HEO 187>: C2A C3A C1A CAA
> <HEO 187>: C2B C3B C1B CMB
> <HEO 187>: C2C C3C C1C CMC
> <HEO 187>: C2D C3D C1D CMD
> <HEO 187>: C3A C4A C2A CMA
> <HEO 187>: C3B C4B C2B CAB
> <HEO 187>: C3C C4C C2C CAC
> <HEO 187>: C3D C4D C2D CAD
> <HEO 187>: C4A NA C3A CHB
> <HEO 187>: C4B NB C3B CHC
> <HEO 187>: C4C NC C3C CHD
> <HEO 187>: C4D ND C3D CHA
> total 627 improper torsions applied
> 20 improper torsions in old prep form
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> 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
>
> CSER 1
> NMET 1
> )
> (no restraints)
>
> On Tue, Jul 11, 2017 at 5:36 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> The program is written to give you advice when there is a problem.
>>
>> The message you seem to not read is telling you to use addAtomTypes.
>>
>> Please try to read all the output carefully for understanding. It was
>> written with you in mind.
>>
>> Bill
>>
>>
>> On 7/11/17 2:30 PM, Rana Rehan Khalid wrote:
>>> No advice in this thread. I check it maybe it is in my previous threads.
>>> Thanks
>>>
>>> On Tue, Jul 11, 2017 at 5:24 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>
>>>> The advice I quoted from your output:
>>>>
>>>> +--- Sp0 probably means a new atom type is involved
>>>> +--- which needs to be added via addAtomTypes
>>>>
>>>> On 7/11/17 2:23 PM, Rana Rehan Khalid wrote:
>>>>> Which one advice Sir
>>>>>
>>>>> On Tue, Jul 11, 2017 at 5:20 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>>>
>>>>>> Did you follow that advice?
>>>>>>
>>>>>> Bill
>>>>>>
>>>>>>
>>>>>> On 7/11/17 2:05 PM, Rana Rehan Khalid wrote:
>>>>>>> +--- Sp0 probably means a new atom type is involved
>>>>>>> +--- which needs to be added via addAtomTypes
>>>>>> _______________________________________________
>>>>>> 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
>>>> _______________________________________________
>>>> 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
>>
>> _______________________________________________
>> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 11 2017 - 15:00:05 PDT
