Re: question about ligand

From: Lishan Yao <>
Date: Sat 1 Feb 2003 21:24:57 -0500 (EST)

   I changed the ligand atoms names in 'pdb' file to the names in prep file.
But it doesn't work. Once LEaP reads revised 'pdb' file, it is just crashed
automatically. This is the information I get.

yaolisha_at_mcbisgi [48] xleap -f leaprc.ff94
-I: Adding /usr/local/amber7/dat/leap/prep to search path.
-I: Adding /usr/local/amber7/dat/leap/lib to search path.
-I: Adding /usr/local/amber7/dat/leap/parm to search path.
-I: Adding /usr/local/amber7/dat/leap/cmd to search path.
-f: Source leaprc.ff94.
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 443
!FATAL: Message: bondAtomProblem found

   Actually, before I revise the 'pdb' file, at least LEaP works fine even
though it complains about the atom names of the ligand and MG. At the
biginning, I tried to fix this problem by using 'edit' in xleap program and
change atom types and charges one by one. And the number of error messages
decreases one when I change one of them. But I don't know whether that's
the right way to fix the problem, and also that's time consuming.
   When I look at the ligand prep file,comparing with 'pdb' file, atom names
are changed from some strange names like 'O1G','O1B', to some ordinary name
like 'O1' and 'O2' (I use guassian output to create the prep file).
   So I don't know what should I do?

Lishan Yao
Lishan Yao

> It is generally better to change the names in the *pdb* file to match those
> in the prep file, but either direction will work. What are the error messages

> LEaP writes out? They are usually pretty informative about what doesn't
> match between the prep and pdb files.
> Send some sample files if you still have problems.
> ..good luck...dac
> --
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> David A. Case | e-mail:
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
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Received on Sat Feb 01 2003 - 18:24:57 PST
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