Hello again Dan
Once again I am super impressed by the willingness to spend time and effort trying to help others solve their issues on this forum, by everyone pitching in.
This may get me part of the way. Realising that what will be suggested is an huge oversimplification, I am right now more curious in getting the method to work rather then the validity of the resulting parameters.
I’ve also come to the conclusion that working with PDB will cause some issues, keeping the connect records helped though it may not be the ideal format for these purposes. I don’t know why though for some reason I did think of using the parm/rst files as also indicated earlier by and was struggling to work with lib/off files and keeping the PDB format.
This seems like a promising way to start, instead of trying to export the required parameters only in combination with PDB I’ll use leap to save parm/rst and have graft deal with the cut-and-paste work, saving mol2 files instead. For the “non-sugar” part, as you have indicated, a quick and dirty way to produce parameters would be antechamber and AM1-BCC. However, instead of trying to modify and work with the prep/frcmod files, follow the above suggested route through leap to prepare parm/rst files for use with cppptraj.
I am sure I will run into some sort of unforeseen problem though this seams like a better route to try to achieve what I am hoping for.
Best regards
// Gustaf
> On 28 May 2021, at 15:25, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi Gustaf,
>
> So I took another look at your molecules, and I have a few thoughts.
> Above all, remember that LEaP is really just a bookkeeping program; it
> only knows what is in the structure you give it and what is in the
> loaded library files. When you load a PDB file, it tries to match
> residue and atom names to the loaded library templates in order to
> assign atom types (which in turn are used to assign parameters). When
> you load a mol2 file, LEaP will try to use the atom types in the mol2
> file.
>
> Since cpptraj doesn't have atom type information when you use PDB
> files as inputs, it has no idea what atom types to use when writing
> the mol2, so it just uses the atom names. This is not going to be
> useful for LEaP, so if you use PDB files as your starting structures,
> writing out as a mol2 probably isn't your best bet. If you go this
> route I would write out a PDB file with the 'conectmode all' option to
> get a PDB with all the correct linkages.
>
> However, you now have a new problem. There is a library file for 4HA
> and ROH, but not NFM (the formamide substituent), at least not as far
> as I know. What's more, the template for 4HA does not have the correct
> linkage set up (it will add an extra oxygen according to the
> template).
>
> So with all this in mind, this is what I was able to do. First, load
> sugar.pdb into leap with glycam, save the topology and restart:
>
> source leaprc.GLYCAM_06j-1
> m = loadpdb sugar.pdb
> saveamberparm m sugar.parm7 sugar.rst7
> quit
>
> Use the topology and restart to load the sugar in cpptraj (instead of
> the PDB) for the graft command. This will ensure that at least the
> atoms for the sugar part will have the right glycam atom types:
>
> parm sugar.parm7
> loadcrd sugar.rst7 parmindex 0 name SUG
> <rest of the graft input>
>
> If you load the resulting mol2 in tleap, the ROH and sugar parts will
> have all their parameters, but you will still be missing parameters
> for the 'NFM' part. If you can't find parameters for NFM,
> unfortunately you'll have to parameterize it yourself. You can try and
> assign the atom types by analogy (in terms of the protein FF H4 can
> probably be H, H7 can probably be H5 which is hydrogen at C with 2
> elec. withdrawing groups, and the heavy atoms can stay as N, C, and O)
> but you'll also need to assign charges. Doing this by analogy is
> probably not a good idea; you will probably have to do the usual
> procedure of creating the NFM fragment, attaching an appropriate
> blocking group, calculating the ESP, doing the RESP fit, etc. You
> could try to get away with just the AM1-BCC charges (via e.g.
> antechamber) since it's a pretty small and inflexible fragment, but
> now we're really getting into more scientific questions and not code
> issues.
>
> There are others on this mailing list who are far more knowledgeable
> about force fields and parameterization, so maybe they will have more
> or better advice. Good luck!
>
> -Dan
>
>
> On Fri, May 28, 2021 at 5:49 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>
>> 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 Mon May 31 2021 - 01:00:02 PDT
