[AMBER] Atome type fatal error

From: Pierre Bertin <bertinp71.gmail.com>
Date: Wed, 6 May 2015 02:20:34 -0600

Hi everyone,

I know that there is a lot a documentation about the LEaP error : Fatal
error ATOM xxx does not have a type.

I found tutorials and reading the manual I am trying to run a simulation of
a large pdb file with a non common residue (CNT ftw!).

The method :

(1) Make separated pdb file :
Protein + CNT and CNT alone.

(2) Antechamber is used in order to convert the pdb file to mol2 file. No
error at this moment.

(3) From the CNT.mol2 file, I use Parmchk2 to generate the CNT.frcmod file.
I do not have any warning or error and I have a frcmod file.

(4) Let's go -> LEaP.


>source leaprc.ff14SB
>source leaprc.gaff
>cnt = loadMol2 CNT.mol2
>loadAmberParams CNT.frcmod
>check cnt :
No warnings, unit ok.

#put the cnt unit in library :
>saveoff cnt cnt.lib
Close tleap.

>source leaprc.ff14SB
>source leaprc.gaff
>loadoff cnt.lib
>loadAmberParams CNT.frcmod
>Complex = loadpdb CNT+prot.pdb
>saveAmberParm Complex C.prmtop C.inpcrd

And when I run this command, I have the 180 atoms of the CNT which are not
typed. But when I did "edit Complex", I had not missing bonds.. The
structure is the right one.
I have tried with the protein (pdb file) alone and the saveAmberParm works
perfectly. I have also tried the CNT alone and the saveAmberParm works

I have tried to import the two molecules separately in LEaP and make the
connections with "bond" command and "restrainBond".. But the same problem
is remaining.

Thank you a lot for you advices or light on this!

​Link : one of the tutorial to import a ligand with protein separately used
--> http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-nonstandard/​

*Pierre BERTIN*
Bioinformatics and Biostatistics student (MSc),
University Paris-Sud XI, ORSAY.
AMBER mailing list
Received on Wed May 06 2015 - 01:30:06 PDT
Custom Search