Thanks to Ben for your help; antechamber in AmberTools 1.5 is running fine, the sustiva example works. Now I am trying to get it to work for my molecule. I am trying to parameterize a macrocyclic lactone antibiotic for Leap, and based on the ATOMTYPE.INF file, the atoms are being identified and bonded correctly, but the antechamber run fails at the sqm step. sqm.out says that there is no convergence in SCF after 1000 steps.
So I guess I have several questions that I couldn't find answers for from the manual or paper.
1) "Bond types are assigned for valence state 14 with a penalty of 2. " From Fig. 5 in the paper, penalty of 2 looks good, but I couldn't figure out where the value of 14 comes from (formula is C37 H59 O11 N).
2) Atoms in the macrolactone ring are not identified as being in a ring, I assume this was because rings are only 3,4,5 and 6 member?
3) Can I increase the number of steps in the SCF run to see if that gives convergence? Failing that, can I force output of a .mol2 file to see where the problems lie, or this info in one of the files I already get?
Thanks again,
Tom Pochapsky
On Jan 9, 2012, at 1:24 PM, Ben Roberts wrote:
> Hi Tom,
>
> On 9/01/2012, at 1:15 PM, Thomas Pochapsky wrote:
>
>> I am new to antechamber, I am trying to parameterize a macrocyclic compound, and am unable to get atom types or even coordinates in my output files, even using the sustiva_h.pdb tutorial example. It looks like a path problem to me, but Amber runs OK, so should I have additional lines in my .cshrc so that antechamber finds the parameters it is looking for?
>>
>> I am providing the input line I used from the tutorial, and the output.
>>
>> input:> antechamber -i sustiva_h-1.pdb -fi pdb -o sustiva_h.mol2 -fo mol2 -c bcc -s 2
>>
>> output:
>> Running: /nmr/Programs/amber/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
>>
>> Total number of electrons: 160; net charge: 0
>>
>> Running: /nmr/Programs/amber/amber8/exe/divcon
>>
>> Running: /nmr/Programs/amber/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /nmr/Programs/amber/amber8/dat/antechamber/BCCPARM.DAT -j 4
>>
>> Cannot successfully assign bond type for this molecule, 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
>
> I see you're still using Amber 8. Antechamber has been re-released a number of times since then, now as part of AmberTools, a free download from http://ambermd.org. You may wish to download AmberTools 1.5 (the most recent version) and try its antechamber.
>
> Regards,
> Ben
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Received on Thu Jan 12 2012 - 08:00:04 PST
