Sorry, just noticed you reply.
After going through all the files the recompiled version did what "pert true” did not, though I am missing the parameters for the last carbon-fe interactions.
So now I just have to make sure that I can generate this missing atom information and everything should work as intended.
Best regards
// Gustaf
> On 13 Aug 2021, at 15:13, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> Do you have these parameters loaded into leap? These are missing
> parameters, it's possible that you didn't see these before if it failed to
> build the bonds.
>
> On Fri, Aug 13, 2021, 7:17 AM 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 - 06:30:03 PDT
