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.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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>
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>
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Received on Wed Feb 04 2009 - 01:11:46 PST
