Hello again Dan
This was my what I was hoping for, however it seems that loading the grafted structure (mol2) into leap using FF/LIB files it should pull parameters in part from GLYCAM and in part from gaff2 (prep/frcmod) based on atom type.
This is not what I am seeing sadly. From what I could tell doing a quick check, most if not all bond and angle parameters are missing for the entire structure. I have limited experience working with mol2 format so I will have to also do a little research there.
I will not have time to dig further into this today though I will continue and try to find a solution that works.
Best regards and thank you
// Gustaf
> On 28 May 2021, at 11:34, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi Gustaf, glad that 'graft' worked for you.
>
> As far as your parameter issue, there are a few things you could try.
> Probably the most straightforward is to load the structure mol2 from
> 'graft' into leap (it should still have all the original atom types),
> note which bonds/angles/dihedrals leap complains are missing
> parameters, then find the best parameters by analogy in
> parm10.dat/parm19.dat (or similar) in $AMBERHOME/dat/leap/parm, or you
> can run the mol2 through antechamber and see what parameters gaff
> assigns to it (or do both and pick what you think is best).
>
> Hope this helps,
>
> -Dan
>
> On Fri, May 28, 2021 at 4:46 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>
>> With some help correcting my input, the graft command worked very well in preparing a “joint” molecular structure by aligning, removing overlapping and “bonding”.
>>
>> This its a really nice addition to CPPTRAJ, should solve some problems aligning and bonding structures.
>>
>> Thank you very much for the tip, tool and the help Dan, much appreciated. This takes care of generating separate structures and the joint structure, maintaining information available in the input files.
>>
>> The remaining problem, for me, is still how to retain the desired parameters from two different FFs when loading this new structure, leaving only the “intersect” with as little manual editing involved as possible.
>>
>> Best regards
>> // Gustaf
>>
>>> On 26 May 2021, at 15:33, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>
>>> Hi,
>>>
>>> On Wed, May 26, 2021 at 5:17 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>>>
>>>> bond :1.CB,:1.C2
>>>>
>>>> Is :1 the now joined molecule? Otherwise, should I provide the correct residue number :2.X,1.X
>>>
>>> No, the bond masks are "<tgt>,<src>" - i.e. they are specific to the
>>> molecules *before* you join everything. So in the above case, it means
>>> "bond atom CB in residue 1 of target to atom C2 in residue 1 of
>>> source". The code will internally update indices to keep track of what
>>> is what after atoms are removed. Hopefully this clears it up, let me
>>> know if not
>>>
>>> -Dan
>>>
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Received on Fri May 28 2021 - 03:00:03 PDT
