You can view them in VMD.
On Tue, Apr 16, 2024, 5:57 AM ABDELATIF MESSAOUDI <amessaoudi.univ-batna.dz>
wrote:
> Dear Carlos
> Thank you for your answer.
> What do I need to do to view the top file and crd file for this PDB (4w93)
> along with its ligand
> attached pdb files
> best regards
>
> Abdelatif
>
> Le mar. 16 avr. 2024 à 02:49, Carlos Simmerling <
> carlos.simmerling.gmail.com> a écrit :
>
>> Is residue PCA the one that is in your ligand library ?
>>
>> You might want to consume usual troubleshooting steps, like attempting to
>> build the ligand alone before trying a complex.
>>
>> On Mon, Apr 15, 2024, 7:17 PM ABDELATIF MESSAOUDI via AMBER <
>> amber.ambermd.org> wrote:
>>
>>> Dear AMBER users,
>>>
>>> I am using PDB file (code pdb :4w93) structure for molecular dynamics
>>> simulation with AMBER22.
>>>
>>>
>>> First I ran the command:
>>>
>>>
>>> - antechamber -i Lig.log -fi gout -o Lig.mol2 -fo mol2 -c resp
>>>
>>> - parmchk -i Lig.mol2 -o Lig.frcmod -f mol2
>>>
>>> after # xleap
>>>
>>> - source leaprc.gaff2
>>>
>>> - source leaprc.protein.ff14SB
>>>
>>> - source leaprc.water.tip3p
>>>
>>> - loadamberparams Lig,frcmod
>>>
>>> - MOL=loadmol2 Lig,mol2
>>>
>>> - a=loadpdb 4w93,pdb
>>>
>>> - check a
>>>
>>> saveamberparm a Lig.top Lig.crd
>>>
>>> quit
>>>
>>> But at the last step, the parameters cannot be saved because of this kind
>>> of errors:
>>> [image: image.png]
>>>
>>> How can this problem be solved?
>>> Thank you for your help.
>>>
>>> Abdelatif
>>> University of Batna
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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Received on Thu Apr 18 2024 - 06:30:01 PDT
