This is because MCPB.py did not catch all the carbons, there are in fact no parameters for the absolutely last carbon and the bond with iron. With the recompiled version allowing 10 bonds, I can get 9/10 then there are missing parameters for the last carbon.
Best regards
// Gustaf
> On 13 Aug 2021, at 14:16, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> I could not find any way to allow for the extra 2 bonds to be generated so far in leap.
>
> I tried to recompile as suggested somewhere on the forum
>
> amber20_src/AmberTools/src/leap/src/leap/atom.h
>
> #define MAXBONDS 8
> -->
> #define MAXBONDS 10
>
> This did not work as intended as I now have a whole series of
>
> Could not find bond parameter for: M1 - c2
> Building angle parameters.
>
> Could not find angle parameter: Z1 - M1 - c2
> Could not find angle parameter: Y4 - M1 - c2
> Could not find angle parameter: Y3 - M1 - c2
> …
> …
>
> Which were not there before! If the number of bonds to the ion in LEaP was the only problem and MCPB.py had generated all the input I needed than I don’t see how this would happen. Everything seems to work just fine if I exclude the last to bonds in the list, so I have no idea if MCPB.py depends on leap during some earlier step or if something else in the code got messed up along the way.
>
> One step forward, two steps back
> Best regards
> // Gustaf
>
>
>> On 13 Aug 2021, at 12:22, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>
>> According to the “set” documentation, the “pert” parameter is not present. This is slightly discouraging
>>
>> // Gustaf
>>
>>> On 13 Aug 2021, at 12:14, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>>
>>>> bond mol.2.FE mol.3.C13
>>> Bond: maximum coordination exceeded on .R<FE1 2>.A<FE 1>
>>> -- setting atoms pert=true overrides default limits
>>>
>>> So I can only do eight. I tried
>>>
>>> set mol.2.FE pert true
>>>
>>> Which executed without complaints though the error persist. I need those 2 final bonds so do I change something in the “set” command or is there a way to solve this problem that I am unaware of?
>>>
>>> Best regards
>>> // Gustaf
>>>
>>>> On 13 Aug 2021, at 12:02, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>>>
>>>> Sadly, no. Parmed only shows 8 bonds where two are missing.
>>>>
>>>>> printBonds :FE1
>>>> Atom 1 Atom 2 R eq Frc Cnst
>>>> 22 C9 ( Z1) 24 FE ( M1) 2.0449 87.0000
>>>> 20 C8 ( Y4) 24 FE ( M1) 2.0519 84.0000
>>>> 18 C7 ( Y3) 24 FE ( M1) 2.0523 83.5000
>>>> 16 C6 ( Y2) 24 FE ( M1) 2.0534 84.9000
>>>> 15 C5 ( Y1) 24 FE ( M1) 2.0480 75.7000
>>>> 24 FE ( M1) 25 C10 ( Y6) 2.0521 85.3000
>>>> 24 FE ( M1) 27 C11 ( Y7) 2.0538 85.1000
>>>> 24 FE ( M1) 29 C12 ( Y8) 2.0539 84.7000
>>>>
>>>> Best regards
>>>> // Gustaf
>>>>
>>>>> On 13 Aug 2021, at 11:56, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>>>>
>>>>> I realised that the “duplicate records” were likely the ones in the TEST_tleap.in file where there are repeating bonds defined to iron:
>>>>>
>>>>> bond mol.1.C5 mol.2.FE
>>>>> bond mol.1.C5 mol.2.FE
>>>>> bond mol.1.C6 mol.2.FE
>>>>> bond mol.1.C6 mol.2.FE
>>>>> bond mol.1.C7 mol.2.FE
>>>>> bond mol.1.C7 mol.2.FE
>>>>> bond mol.1.C8 mol.2.FE
>>>>> bond mol.1.C8 mol.2.FE
>>>>> bond mol.1.C9 mol.2.FE
>>>>> bond mol.1.C9 mol.2.FE
>>>>> bond mol.1.C9 mol.2.FE
>>>>> bond mol.1.C9 mol.2.FE
>>>>> bond mol.2.FE mol.3.C10
>>>>> bond mol.2.FE mol.3.C10
>>>>> bond mol.2.FE mol.3.C11
>>>>> bond mol.2.FE mol.3.C11
>>>>> bond mol.2.FE mol.3.C12
>>>>> bond mol.2.FE mol.3.C12
>>>>> bond mol.2.FE mol.3.C13
>>>>> bond mol.2.FE mol.3.C13
>>>>>
>>>>> So I kept the “gaff2” source in and removed all the duplicate entries:
>>>>>
>>>>> bond mol.1.C5 mol.2.FE
>>>>> bond mol.1.C6 mol.2.FE
>>>>> bond mol.1.C7 mol.2.FE
>>>>> bond mol.1.C8 mol.2.FE
>>>>> bond mol.1.C9 mol.2.FE
>>>>> bond mol.2.FE mol.3.C10
>>>>> bond mol.2.FE mol.3.C11
>>>>> bond mol.2.FE mol.3.C12
>>>>> bond mol.2.FE mol.3.C13
>>>>>
>>>>> This seems to have worked though in the mcpb.in file I defined 10 bonds:
>>>>>
>>>>> add_bonded_pairs 24-15 24-16 24-18 24-20 24-22 24-25 24-27 24-29 24-31 24-22
>>>>>
>>>>> and I cannot help but notice that there are only 9 bonds added here. In VDM the “FE1.FE 3.C13” nondescripts is not visualised, I am only seeing eight. I manually added the missing " bond mol.2.FE mol.3.C14” to the input
>>>>>
>>>>> bond mol.1.C5 mol.2.FE
>>>>> bond mol.1.C6 mol.2.FE
>>>>> bond mol.1.C7 mol.2.FE
>>>>> bond mol.1.C8 mol.2.FE
>>>>> bond mol.1.C9 mol.2.FE
>>>>> bond mol.2.FE mol.3.C10
>>>>> bond mol.2.FE mol.3.C11
>>>>> bond mol.2.FE mol.3.C12
>>>>> bond mol.2.FE mol.3.C13
>>>>> bond mol.2.FE mol.3.C14
>>>>>
>>>>> By removing duplicates I was also able to drop the "set mol.2.FE pert true” part, this is no longer needed.
>>>>>
>>>>> cpptraj -p TEST_solv.prmtop
>>>>>
>>>>> Now produces no errors. However, VMD still does not visualise all 10 bonds to FE, only 8. I have experienced before other visualisation issue before and my hope is that this is only a visualisation problem?
>>>>>
>>>>> Best regards
>>>>> // Gustaf
>>>>>
>>>>>> On 13 Aug 2021, at 11:17, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>>>>>
>>>>>> After some work I managed to get through steps 2-4 of MCPB though now I am stuck at the tleap step.
>>>>>>
>>>>>> I have all the files that are indicated and these generally look to be OK. I ran tleap with the generated input file and received repeats of to general errors:
>>>>>>
>>>>>> Bond: Maximum coordination exceeded on .R<FE1 2>.A<FE 1>
>>>>>> -- setting atoms pert=true overrides default limits
>>>>>>
>>>>>> and
>>>>>>
>>>>>> amber20/bin/teLeap: Error!
>>>>>> For atom (.R<LG1 1>.A<C1 1>) could not find vdW (or other) parameters for type (c2)
>>>>>>
>>>>>> I figured the latter one is because i only have non-amino acid residues parameterised using gaff2 with antechamber and parmchk2. So I added a line sourcing gaff2 in the TEST_tleap.in file producing an additional error:
>>>>>>
>>>>>> !FATAL ERROR----------------------------------------
>>>>>> !FATAL: In file [/Users/guolaa/SOFTWARE/amber20_src/AmberTools/src/leap/src/leap/unitio.c], line 1808
>>>>>> !FATAL: Message: 1-4: cannot add bond 20 24
>>>>>> This may be caused by duplicate bond specifications;
>>>>>> for example, explicit bond commands in addition to PDB conect records.
>>>>>> !
>>>>>> !ABORTING.
>>>>>>
>>>>>> There are no connect records in the TEST_mcbppy.pdb file generated and while this error message obviously refers to the same issue, is a lot less informative then the repeating instances of the error above, carbon bonds to ion. I really need a win here to end the week on a good note :)
>>>>>>
>>>>>> 1) Can I assume that I am correct that “source.leaprc.gaff2” needs to be added to the TEST_tleap.in file?
>>>>>>
>>>>>> 2) Is the " !FATAL ERROR” likely caused by the "Bond: Maximum coordination exceeded” problem?
>>>>>>
>>>>>> I am trying to figure out how to use “set” to include the "pert=true” as suggested though have not managed to figure it out just get.
>>>>>>
>>>>>> As usual I am attaching my files in hope of some helt identifying and hopefully solving this problem.
>>>>>>
>>>>>> Best regards
>>>>>> // Gustaf
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> <FE1.mol2><LG1.mol2><LRG.frcmod><SL1.mol2><SML.frcmod><TEST_mcpbpy.frcmod><TEST_mcpbpy.pdb><TEST_tleap.in>_______________________________________________
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>>>>>
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Received on Fri Aug 13 2021 - 06:30:02 PDT
