[AMBER] Maximum coordination exceeded

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Fri, 13 Aug 2021 09:17:16 +0000

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


   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.

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

AMBER mailing list

Received on Fri Aug 13 2021 - 02:30:02 PDT
Custom Search