BTW, this LEaP tutorial can be helpful for you to understand the molecular recognition in LEaP.
> On Jul 22, 2019, at 9:48 PM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
> Hi Sarah,
>
> I think you only need to change the atom types in the second and third mol2 and frcmod files. Meanwhile, you need to change the MCPB.py generated mol2 file names of the second HEME site residues to prevent conflicts.
>
> In these modifications, only atom types of the metal ligating atoms need to be changed.
>
> Hope it helps,
> Pengfei
>
>> On Jul 15, 2019, at 6:59 PM, SARAH JEANNE LEFAVE <s.lefave.utah.edu> wrote:
>>
>> Thanks Pengfei!
>>
>> The method I have been using is very similar to the sed command. Just to clarify, should I be changing the atom name or the atom type (the capital or lower case letters in the mol2 files) or both? I tried both and then tried to do each individually. Although, I think I probably introduced additional errors along the way, I wanted to check before re-doing all those options. It would be simpler to only have to one if that’s all that’s needed. Additionally, in the *.mol2 files generated for residues in the active site, e.g HD1.mol2 for a coordinated histidine to the heme, both the atom name and type are capitalized and some of the names are the same notation as the type (specifically the backbone N and some others). Should I keep those the same or introduce new names/types for those as well?
>>
>> Thank you again for the help,
>> Sarah
>>
>>> On Jul 9, 2019, at 8:45 PM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>>>
>>> Hi Sarah,
>>>
>>> The strategy of renaming some atom types was correct but this process can be complicated due to so many new atom types you have now.
>>>
>>> One suggestion is to use the “sed" command to rename the atom types in the second and third of the MCPB.py generated frcmod files (e.g. replacing M1 by M2, etc) to prevent parameter conflicts and human errors, and do not combine these frcmod files but read them separately in the final LEaP input file.
>>>
>>> Hope it helps,
>>> Pengfei
>>>
>>>> On Jul 5, 2019, at 1:13 PM, SARAH JEANNE LEFAVE <s.lefave.utah.edu> wrote:
>>>>
>>>> Hi all,
>>>>
>>>> I am parameterizing a protein with 3 different metal centers (two heme sites with different charges on the metal and substituents, and a Cu histidine site) I have finished MCPB.py steps 1-4 and am working on generating the parameter and topology files. I ran 3 separate MCPB.py runs for each of the metal sites as they are distinct active sites from one another. This generated 3 different sets of files for running with tleap. I combined these into one protein_tleap.in adding the additional atoms to be defined and loading all the relevant files in. After getting many errors about **no angle parameters and ** not torsion terms, I redefined the redundant metals and nitrogen’s that were added in the addAtomTypes section such that I now have (M1-M3 and Y1-14). I also modified the mol2 and frcmod files to be consistent for these. While this reduced some of the errors regarding angle parameters and torsion terms I still get a significant amount. I suspect it is due to the redundant cc, ce, cd, ha… and CR, CV, HX… etc. If this is in fact the problem is there another way to change this rather than manually renaming the atoms in the ligand? Will renaming them to non-redunant names cause any other error for recognition with gaff or otherwise?
>>>>
>>>> Thank you!
>>>> Sarah
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Received on Mon Jul 22 2019 - 19:00:02 PDT
