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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Received on Fri Aug 13 2021 - 03:00:02 PDT
