AMBER Archive (2009)

Subject: Re: [AMBER] RE: Tutorial 5

From: George Tzotzos (gtzotzos_at_mac.com)
Date: Sun Feb 01 2009 - 15:04:36 CST


Hi Ross,

Many thanks, much appreciated. I'll try your suggestions tomorrow and
if anything untoward occurs, I'll report it to the list.

All the best

George

On Jan 31, 2009, at 2:32 AM, Ross Walker wrote:

> 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 |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery,
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