Dear Mark,
Let's see what we can do here...
First, are you sure you want to protonate the aldehyde oxygen to an oxonium
ion???? (-C=O-H)
+
If so, then lets take a look. The gaff parameters that antechamber gives
for your main chain using your pdb file are wrong, since the program needs
to "guess" atom types from your "coordinates only" pdb file. To demonstrate
this problem, I put your pdb file into 2 different chemical structure
drawing programs, and got two different sets of double bond locations!
So, first I loaded your pdb structure in VegaZZ (my chemical structure
program of choice), and explicitly put the double bonds in the correct
places. Then I minimized your structure in mopac (PM6). Then I saved as a
mol2 file. I input this mol2 file (retchmopac.mol2) to antechamber, since I
get the best shot at getting the atom types correct using mol2 files as
inputs to antechamber.
The output mol2 file, retchbbc.mol2 has all the correct atom types for a
conjugated chain of carbons (ce and cf atom types), and a check with parmchk
did not find any situation it couldn't handle, and gives a frcmod with
reasonable parameters.
Of course, this is just a starting point. The oxonium is typed as a
traditional OH oxygen, so I would be a bit suspicious of bond length there,
etc.
I hope this helps... and good luck with your work!
Dean
> From: case <case.biomaps.rutgers.edu>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Tue, 5 Jan 2010 22:36:15 -0600
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] antechamber bond type error
>
> On Tue, Jan 05, 2010, Mark M Huntress wrote:
>>
>> antechamber -i retch.pdb -fi pdb -o retch.mol2 -fo mol2 -c bcc
>>
>> The error was:
>>
>> Warning: the assigned bond types may be wrong, please :
>> (1) double check the structure (the connectivity) and/or
>> (2) adjust atom valence penalty parameters in APS.DAT, and/or
>> (3) increase MAXVASTATE in define.h and recompile bondtype.C
>> (4) increase PSCUTOFF in define.h and recompile bondtype.C
>>
>>> Hi, I am trying to parameterize a molecule (protonated, positively
>>> charged retinal) and I am getting the following error when I put in the
>>> following input:
>
> Since your molecule is a cation, you have to include the "-nc 1" flag
> to tell antechamber that this is an ion; by default it assumes that the
> molecule has no net charge. Also, when you have problems with the default
> "-j 4" flag, it is often good to try "-j 5". Hence for me, the command:
>
> antechamber -i retch.pdb -fi pdb -o retch.mol2 -fo mol2 -c bcc -nc 1 -j 5
>
> gives a reasonable-looking mol2 file. (Be sure to check for yourself:
> antechamber results, especially for polyenes, should be viewed as a good first
> step, not as gospel. It doesn't know about fractional bond orders, but those
> are not used by Amber anyway. However, torsional barriers to rotation
> predicted by GAFF for a highly delocalized system like this one are unlikely
> to be reliable; I don't know if this is important for what you want to do or
> not.)
>
> ...hope this helps...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 05 2010 - 22:00:03 PST
