Thanks Bill, I was able to fix it through a tutorial.
And thank you to the rest of responders to my thread.
——
Jatin Kashyap
Ph.D. Student
Dr. Dibakar Datta Group
Department of Mechanical and Industrial Engineering
New Jersey Institute of Technology (NJIT)
University Heights
Newark, NJ 07102-1982
Phone- (201)889-5783
Email- jk435.njit.edu
> On Jan 6, 2021, at 3:48 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> Hi Jatin,
>
> Try searching on 'amber ligand demo'. Amusingly, my first google hit is
> a charmm demo w/ amber ff, but there are more. I'd say browse all the
> tutorials as well, so you know what to copy from when in doubt.
>
> Bill
>
> On 1/5/21 10:28 PM, Jatin Kashyap wrote:
>> Hi Bill,
>>
>> Yes, I am new to AMBER and never did this mapping.
>> Can you please point out some tutorials which I can follow.
>>
>> Thanks.
>>
>>
>> ——
>> Jatin Kashyap
>> Ph.D. Student
>> Dr. Dibakar Datta Group
>> Department of Mechanical and Industrial Engineering
>> New Jersey Institute of Technology (NJIT)
>> University Heights
>> Newark, NJ 07102-1982
>> Phone- (201)889-5783
>> Email- jk435.njit.edu
>>
>>> On Jan 6, 2021, at 12:51 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>
>>> This implies you have unusual atom types in LIG, which is common for
>>> user-built residues.
>>>
>>> Look into the atom types for those atoms, map them to VDW params in
>>> whatever forcefield you are using, and you'll have your culprit, as sure
>>> as there's fog in London. OR if you're new to Amber, it might be easier
>>> to look closely at a tutorial or two.
>>>
>>> Bill
>>>
>>>
>>> On 1/5/21 9:09 PM, Jatin Kashyap wrote:
>>>> Hi David,
>>>>
>>>> I followed this procedure and I found three couples of atoms which have 0 Ang distance as shown below[1].
>>>> And here is my observation: I am feeding the complex[2] and ligand[3] pdb files as described in the Amber tutorial[4].
>>>> Everything is fine with input pdb files i.e. no overlap BUT the output complex pdb file[5] that I obtained at the end of the step “Creating topology and coordinate files for Sustiva-RT complex”
>>>> of the tutorial is giving my those three couples of atoms which have exactly same coordinates to each other. Prmtop and rst7 files obtained form same step were used for CPPTRAJ instructions[1].
>>>>
>>>>
>>>>
>>>> [1]
>>>> 1 Warning: Atoms 1:LIG_1.N and 20:LIG_1.N3 are close (0.00)
>>>> 1 Warning: Atoms 4:LIG_1.C and 22:LIG_1.C13 are close (0.00)
>>>> 1 Warning: Atoms 17:LIG_1.O and 18:LIG_1.O1 are close (0.57)
>>>> 1 Warning: Atoms 17:LIG_1.O and 23:LIG_1.O3 are close (0.00)
>>>> .
>>>> .
>>>> ...
>>>>
>>>> [2]
>>>> https://drive.google.com/file/d/1ZcZWthwZgSzE6WcGsMQEMh6WKlGs_l84/view?usp=sharing
>>>>
>>>> [3]
>>>> https://drive.google.com/file/d/1Viw3AZKaBZ1JeK6-ZvtXxzduUhEqmQOH/view?usp=sharing
>>>>
>>>> [4]
>>>> https://ambermd.org/tutorials/basic/tutorial4b/index.php <https://ambermd.org/tutorials/basic/tutorial4b/index.php>
>>>>
>>>> [5]
>>>> https://drive.google.com/file/d/1S8CDlDIRHUr-CloX3N1AcmPeRyMEpGi_/view?usp=sharing
>>>> ——
>>>> Jatin Kashyap
>>>> Ph.D. Student
>>>> Dr. Dibakar Datta Group
>>>> Department of Mechanical and Industrial Engineering
>>>> New Jersey Institute of Technology (NJIT)
>>>> University Heights
>>>> Newark, NJ 07102-1982
>>>> Phone- (201)889-5783
>>>> Email- jk435.njit.edu
>>>>
>>>>> On Jan 5, 2021, at 10:44 PM, David A Case <david.case.rutgers.edu> wrote:
>>>>>
>>>>> On Tue, Jan 05, 2021, Jatin Kashyap wrote:
>>>>>> I am getting an error[1] upon performing minimization of drug-protein
>>>>>> complex by using the AMBER tutorial[2].
>>>>> You have two atoms on top of one another in your starting structure:
>>>>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>>>>> 1 NaN NaN 9.2217E+09 O1 18
>>>>>>
>>>>>> BOND = 13750.1241 ANGLE = 10976.5308 DIHED = 2934.9414
>>>>>> VDWAALS = NaN EEL = Infinity EGB = 60228.2741
>>>>>> 1-4 VDW = 381037.7111 1-4 EEL = 14860.5376 RESTRAINT = 0.0000
>>>>> Dave Cerutti pointed you to mdgx, but (for me) it's much simpler just
>>>>> to use the cpptraj "check" command: it will print out short non-bonded
>>>>> contacts and bad bonds (the two most common problems with initial
>>>>> structures.)
>>>>>
>>>>> cpptraj <prmtop file>
>>>>> trajin <inpcrd file>
>>>>> check
>>>>> go
>>>>>
>>>>> ....dac
>>>>>
>>>>>
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Received on Thu Jan 07 2021 - 11:30:02 PST
