Hi Ross,
Many thanks. It did work as per your suggestion. However, I have one (I hope) remaining question.
I now have a ligand in mol2 that check OK in xleap. I also have the protein.pdb file which also check OK in xleap. The question is how do I treat the <complex.pdb>. Somehow, I need to append after the TER label the coordinates of the ligand as well as the atom types that were worked out from antechamber. The problem, as I see it, is that the ligand is in mol2.
Solution?
Many thanks in advance
George
On Monday, January 19, 2009, at 04:46PM, "Ross Walker" <ross.rosswalker.co.uk> wrote:
>Hi George,
>
>> I'm loading on xleap a protein/ligand complex obtained from a docking
>> simulation using AutoDock v.4.
>>
>> When I do a check in xleap I get the following fatal errors:
>>
>> WARNING: The unperturbed charge of the unit: -8.000000 is not zero.
>> FATAL: Atom .R<UNK 126>.A<C 1> does not have a type.
>> FATAL: Atom .R<UNK 126>.A<O 2> does not have a type.
>>
>> The ligand is a simple unsaturated aliphatic aldehyde.
>
>You need to provide parameters and charges for the aliphatic aldehyde since
>it is not part of the standard library (amino acids and dna / rna etc). The
>simplest way to do this is to use the GAFF force field and antechamber. The
>following tutorial gives an example of using this:
>http://ambermd.org/tutorials/basic/tutorial4/
>
>You will need to build a pdb file containing just your ligand with the
>hydrogens in place as well. You may also want to consider naming it
>something other than UNK (3 letters max) although in your case since you
>only have this one non-standard residue having it named UNK will not cause a
>problem.
>
>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 |
>
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Received on Wed Jan 21 2009 - 01:11:43 PST
