Thanks it solved the error. But now I am getting another error in MD run “ERROR: I could not find enough velocities in 01.min.rst7"
I am following solution provided here “
http://archive.ambermd.org/201611/0394.html” by inserting “irest=0” in MD script but it is still throwing the same error.
Thank you.
——
> On Jun 30, 2020, at 3:10 AM, Elvis Martis <elvis_bcp.elvismartis.in> wrote:
>
> You could try deleting all hydrogens from your protein and then load it in
> leap.
>
> On Tuesday, June 30, 2020, Jatin Kashyap <jk435.njit.edu> wrote:
>
>> Dear AMBER Users,
>>
>> I am trying to follow tutorials provided by one of the research group from
>> Stony Brook University (http://ringo.ams.stonybrook.
>> edu/index.php/2019_AMBER_tutorial_with_PDBID_2BXF).
>>
>> When I am using Tleap module and issues below commands[1] , It throws the
>> following errors[2] :
>>
>> [1]
>>
>> ###Write Solvated topology and coord file
>> saveamberparm solvcomplex 2BXF.wet.complex.prmtop 2BXF.wet.complex.rst7
>>
>>
>>
>> [2]
>> Created a new atom named: HN within residue: .R<THR 304>
>> Created a new atom named: HN within residue: .R<PHE 305>
>> Created a new atom named: HN within residue: .R<CGLN 306>
>> Added missing heavy atom: .R<CGLN 306>.A<OXT 18>
>> total atoms in file: 2888
>> Leap added 2096 missing atoms according to residue templates:
>> 1 Heavy
>>
>> ….
>> …
>> ….
>> FATAL: Atom .R<PHE 3>.A<HN 21> does not have a type.
>> FATAL: Atom .R<GLY 2>.A<HN 8> does not have a type.
>> FATAL: Atom .R<NSER 1>.A<HN3 16> does not have a type.
>> FATAL: Atom .R<NSER 1>.A<HN2 15> does not have a type.
>> FATAL: Atom .R<NSER 1>.A<HN1 14> does not have a type.
>>
>> /opt/amber/18/bin/teLeap: Fatal Error!
>> Failed to generate parameters
>>
>> Exiting LEaP: Errors = 1; Warnings = 646; Notes = 0.
>>
>>
>> Can anybody please help or provide any other tutorial to perform
>> protein-ligand minimization.
>> Thank you.
>>
>> ——
>> Jatin Kashyap
>>
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> Best Regards
> Elvis
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Received on Tue Jun 30 2020 - 13:30:03 PDT
