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 - 03:30:03 PDT
