AMBER Archive (2005)

Subject: AMBER: An atom name with 4 characters is not compatible with Leap ?

From: Arnoult, Eric [PRDFR] (EArnoult_at_prdfr.JNJ.com)
Date: Fri Jul 22 2005 - 02:53:24 CDT


Dear All,
 
I prepare the "prep" file for several ligands with antechamber.
When the ligand contains an halogen atom (CL for example), the atom name for
this halogen atom is wrote with 4 characters.
 
Then, I load this "prep" file in Leap. An atom name with 4 characters seems
to be not compatible with Leap because I obtained an error message :
"FATAL: Atom .R<lig 276>.A<CL2> does not have type"
 
If I edit the "prep" file and modify the atom name from CL29 to CL2, I
successfully pass this step.
Is it a bug or limitation ? What should I do ? Did somebody modify the
antechamber's code or leap's code for this problem ?

 

Many Thanks
 
 
Best regards
 
Eric ARNOULT
 
 
 
my prep.in :
0 0 2

This is a remark line

molecule.res

lig INT 0

CORRECT OMIT DU BEG

0.0000

1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000

2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000

3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000

...

51 CL29 cl M 50 48 46 1.758 120.465 177.991 -0.04408

 ...
 

IMPROPER

...

C26 C28 C27 CL29

DONE

 

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