AMBER Archive (2009)

Subject: [AMBER] RE: Tutorial 5

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jan 30 2009 - 19:32:03 CST

Hi George,

I didn't see any attachment with your email however, I'll try and help out.
Note you may want to send this message to the amber mailing list (see
http://lists.ambermd.org/) for details since then the actual antechamber
author etc might be able to help.

> I tried to follow the convention you followed in Tutorial 5
> (sustiva.pdb) that is renaming the atoms sequentially:
> C ------> C1
> HC-----> H1
> HC------>H2
> C-------->C2
> etc.
>
> Obviously this is not the right thing because antechamber aborts "
> giving
>
> ---Judge bond type for Residue 1 with ID of 4 and Name of UN ---
> Error: cannot run "/usr/local/amber10/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit"
>
> Is there a rule for renumbering atoms? Should I ignore the warning of
> duplicate atoms and proceed with the parameter files generated from
> the original pdb file (I'm attaching it for easy reference).

I suspect the problem may be that you have altered the spacing of the pdb
file. In PDB files the column alignment and whitespacing is very important
so if things go in the wrong column they can cause problems / misreads etc.
I assume the residue name is UNK for unknown but in the error message above
antechamber is referring to it as UN which suggests it has been moved one
column to the right. Take a look at the pdb file from the tutorial and make
sure all you columns in your pdb align with those in the tutorial pdb. I
don't have the pdb specs to hand right now but typically atom names are left
aligned (except for H's which can have a number in the left-1 column) and
occupy 3 spaces. Thus a single letter name would be "C " while the C1 you
have above would be "C1 " - hence I think using your notation you want:

C ------>C1
HC------>H1
HC------>H2
C------->C2

This should then work fine. You might also want to change the 3 letter
residue name to something else (still 3 letters) just to be more descriptive
- but not a residue name currently used (so no Amino acid or DNA/RNA names
for example).

Try that and see how it does. As for ignoring duplicate atoms I'm not sure
what antechamber actually does here, whether it truly ignores them or
creates 'new' atoms in the form leap does. If you wanted to check the best
option is to load the prep/mol2 file produced from antechamber into xleap
and then do edit UNK (or whatever the residue name is) and see if it comes
up looking correct and with the correct bonds etc. If it doesn't then you
need to go back and make sure antechamber recognizes things correctly.

Good luck,
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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