[AMBER] Problem with covalently bonded ligand parametrization

From: Gustavo Avelar Molina <gustavoavelarmolina.usp.br>
Date: Sat, 23 May 2015 02:07:43 +0000

Hi everyone,

I'm trying to parameterize a molecule that is covalently bonded to a
protein, but I've got stuck when I tried to load the protein+ligand pdb
file, before the step of topology and coordinate files creation. I'm using
the sustiva-RT complex tutorial as a reference. I've obtained the
protein+pdb file by using the fuse command in PyMol to bond the ligand to
the protein.

So, when I use the command:

x = loadpdb AcryCys2.pdb

I get a lot of messages like:

Added missing heavy atom: .R<NTRP 254>.A<O 26>

That I don't know if it's normal, since this is the first time that I try
to use AMBER.

At the end, I receive this message:

Bond: Maximum coordination exceeded on .R<ACR 223>.A<H6 31>
      -- setting atoms pert=true overrides default limits
ATOMS NOT BONDED: .R<ACR 196>.A<C5 12> .R<ACR 223>.A<H6 31>
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 445
!FATAL: Message: bondAtomProblem found

What can I be doing wrong? I would appreciate some help.

With regards,

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Received on Fri May 22 2015 - 19:30:03 PDT
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