You have
...
ATOM 19 O21 0GB 1 6.500 2.115 -1.901 1.00
0.00 O
ATOM 20 H22 0GB 1 5.632 1.856 -1.567 1.00
0.00 H
ATOM 21 O23 0GB 1 5.282 -0.385 -2.359 1.00
0.00 O
ATOM 22 H24 0GB 1 4.824 0.294 -1.828 1.00
0.00 H
ATOM 23 C25 UNK 2 5.022 3.662 -9.358 1.00
0.00 C
ATOM 24 N26 UNK 2 4.804 4.566 -10.043 1.00
0.00 N
ATOM 25 C27 UNK 2 6.665 1.899 -8.925 1.00
0.00 C
ATOM 26 H28 UNK 2 7.461 2.619 -8.729 1.00
0.00 H
ATOM 27 H29 UNK 2 6.653 1.658 -9.992 1.00
0.00 H
ATOM 28 H30 UNK 2 6.870 0.983 -8.368 1.00
0.00 H
ATOM 29 C31 UNK 2 4.175 1.460 -8.687 1.00
0.00 C
ATOM 30 H32 UNK 2 4.068 1.209 -9.746 1.00
0.00 H
ATOM 31 H33 UNK 2 3.228 1.862 -8.322 1.00
0.00 H
ATOM 32 H34 UNK 2 4.409 0.545 -8.139 1.00
0.00 H
ATOM 33 O35 UNK 2 5.381 2.953 -7.150 1.00
0.00 O
ATOM 34 C36 UNK 2 5.309 2.491 -8.473 1.00
0.00 C
And you have a I1-lig.prep for the 0GB residue:
This is a remark line
molecule.res
0GB INT 0
CORRECT OMIT DU BEG
0.0000
(The atom naming follows an odd numbering scheme.)
But you have no prep file for the UNK residue. Why is that? I'd give it
a more descriptive name if it's supposed to be there.
Bill
On 10/18/18 12:18 AM, senal dinuka wrote:
> As per your suggestion I prepared the prep file and separately carried out
> tleap for the ligand portion only. connectivity and naming for sugar
> portion named 0GB is shown to be available but for the portion of ligand
> named UNK, it is still missing. Here I have attached the extracted ligand,
> prep file and its tleap script. Is it possible to work with two residue
> names like here. If so am I doing it the correct way? I appreciate your
> suggestion
>
> Regards,
>
> On Thu, Oct 18, 2018 at 10:16 AM Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> > FATAL: Atom .R<UNK 468>.A<C36 12> does not have a type.
>>
>> Looks like you didn't create a template for your residue? See tutorials
>> (biotin might be good). Res/atom names must match between template and pdb.
>>
>> > Could not find bond parameter for: Cg -
>>
>>> Could not find angle parameter: Cg - Cg -
>> It looks like a blank-space atom type might have slipped through
>> Interpol's net. Maybe if you fix the residue template, you will be able to
>> fix that from the experience.
>>
>> Bill
>>
>> On 10/17/18 9:34 PM, senal dinuka wrote:
>>> I have been trying to generate prmtop and inpcrd files for the below
>>> mentioned receptor/ligand complex. The ligand is a TS structure hence the
>>> weird bond lengths. I was told to use GLYCAM for the sugar portion and
>>> separate frcmod for the cyanogenic part of the ligand since GLYCAM doesnt
>>> offer parameters for the later. Hence I generated a l1.frcmod with bcc
>>> charge scheme through antechamber and parmchk modules with default
>> options.
>>> frcmod seem to be lack in bond and angle properties. And thus the leap
>>> results in error I assumed. I appreciate your guidance regarding the
>> matter.
>>> Thank you
>>> P.S I have attached the complex, ligand as well as frcmod and leap
>> script I
>>> used
>>>
>>>
>>>
>>>
>>> _______________________________________________
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>
>
>
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Received on Thu Oct 18 2018 - 00:30:03 PDT
