Antechamber from AmberTools13 is giving an error: " cannot run "..../sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit" "
I have installed AmberTools13 (http://ambermd.org/#AmberTools) in "/home/uttam/bin" and set AMBERHOME variable as "/home/uttam/bin/amber12". But antechamber is not working. Here is the set of commands and their outputs :
1) `which antechamber(sqm)` => /home/uttam/bin/amber12/bin/antechamber(sqm)
2) `echo $AMBERHOME` => /home/uttam/bin/amber12
3) `locate mopac.sh` => /home/uttam/bin/amber12/AmberTools/src/antechamber/mopac.sh
4) `antechamber -i FFF.pdb -fi pdb -o FFF.mol2 -fo mol2 -c bcc` =>
"Running: /home/uttam/bin/amber12/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/home/uttam/bin/amber12/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit"
5) `antechamber -i FFF.pdb -fi pdb -o FFF.mol2 -fo mol2 -c bcc -df 0` =>
"Running: /home/uttam/bin/amber12/bin/mopac.sh
sh: 1: /home/uttam/bin/amber12/bin/mopac.sh: not found
Error: cannot run "/home/uttam/bin/amber12/bin/mopac.sh" of bcc() in charge.c properly, exit"
What is wrong? How can I get antechamber working?
Hello Uttam,
I believe mopac is no longer supported in AmberTools, and sqm is the "go-to" quantum mechanics program within the package. I would suggest looking at the sqm.out file to start diagnosing your error. My guess is that your input structure either contains an atom(s) that is unsupported by sqm, the input conformation is very poor and never reaches the program's default convergence criteria, the input molecule is too large for QM optimization, or there is a discrepancy between the multiplicity and molecular charge.
Reading up more about sqm in the AmberTools's manual and searching Amber's listserve should give you some additional information to work off of.
Best regards,
Karl
Hello Uttam,
I believe mopac is no longer supported in AmberTools, and sqm is the "go-to" quantum mechanics program within the package. I would suggest looking at the sqm.out file to start diagnosing your error. My guess is that your input structure either contains an atom(s) that is unsupported by sqm, the input conformation is very poor and never reaches the program's default convergence criteria, the input molecule is too large for QM optimization, or there is a discrepancy between the multiplicity and molecular charge.
Reading up more about sqm in the AmberTools's manual and searching Amber's listserve should give you some additional information to work off of.
Best regards,
Karl
I was trying to test acpype (http://code.google.com/p/acpype/) with the pdb structures in its test folder and giving me the error. But it is working fine with other structures while running antechamber with sqm. May be there are some problems in their structures as Karl said. Thanks.
Hello again,
I took a look at your structure and sqm.out file. This is a very large molecule to be running through antechamber. Plus, the molecule is a zwitterion. Zwitterions are somewhat problematic when it comes to quantum gas-phase optimization. It is known that when the zwitterionic functional groups are closely space in x,y,z coordinates, a proton will transfer and form the nonzwitterionic species. This has been seen several times in QM studies of the zwitterionic form of glycine. This may not occur for the conformation shown for your molecule, but it could be contributing to the QM optimization problem. According to the sqm output file, the default number of cycles for achieving a self consistent field (i.e. SCF) was reached, and the calculation aborted. Typically, bigger molecules require more SCF cycles at the beginning of at optimization, especially if the initial conformation is far from a local minima. The AmberTools' manual should have a section informing you how to increase the number of SCF cycles.
However, I would suggest that you reconsider why you are trying to run a short peptide composed three phenylalanines through antechamber, and why the zwitterion ionic form rather than a neutral from using the ACE and NME capping residues. Amber already has all of these residues within its database, along with assigned atom types and balanced partial atomic charges. These are compatible with Amber's force fields; if you alter the partial atomic charges for phenylalanines, then you will be stepping into uncharted territory for how well the force field will model your peptide. This is typically not recommended. Antechamber was designed to help researchers derive models for nonstandard molecules (e.g. drugs). A more rigorous way of deriving the partial atomic charges is using R.E.D., while Wolf2Pack can assist in checking and optimizing any missing parameters within the Amber force fields.
Here are some citations that you may find interesting:
1. Kirschner, K. N.; Lewin, A. H. & Bowen, J. P. Molecular mechanics force-field development for amino acid zwitterions Journal of Computational Chemistry, 2003, 24, 111-128 and reference within.
2. Bayly, C. I.; Cieplak, P.; Cornell, W. & Kollman, P. A. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: the RESP Model Journal of Physical Chemistry, 1993, 97, 10269-10280
2. Cieplak, P.; Cornell, W.; Bayly, C. & Kollman, P. Aplication of the Mulimolecule and Multiconformational RESP Methodology to Biopolymers - Charge Derivation for DNA, RNA, and Proteins Journal of Computational Chemistry, 1995, 16, 1357-1377
3. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W. & Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules Journal of the American Chemical Society, 1995, 117, 5179-5197
4. Dupradeau, F.-Y.; Cézard, C.; Lelong, R.; Stanislawiak, &E.; Pêcher, J.; Delepine, J. C. & Cieplak, P. R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries Nucleic Acids Research, 2008, 36, D360-D367
5. Dupradeau, F.-Y.; Pigache, A.; Zaffran, T.; Savineau, C.; Lelong, R.; Grivel, N.; Lelong, D.; Rosanski, W. & Cieplak, P. The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building Phys Chem Chem Phys, 2010, 12, 7821-7839
6. Krämer-Fuhrmann, O.; Neisius, J.; Gehlen, N.; Reith, D. & Kirschner, K. N. Wolf2Pack -- Portal Based Atomistic Force-Field Development Journal of Chemical Information and Modeling, 2013, 53, 802-808
Best Regards,
Karl
Thanks for your reply. Actually I need GROMOS96 topology of a drug molecule (piroxicam). I have generated this topology using ATB server (http://compbio.chemistry.uq.edu.au/atb/). As suggested in literature (http://pubs.acs.org/doi/abs/10.1021/ci100335w) , charge assignment by automated topology builder is not reliable and charge assignment by AM1-BCC method is very much comatible to GROMOS96 force field. I am trying to use antechamber to calculate partial charges of piroxicam. I installed AmberTools13 and ACPYPE. I used those structure just for testing. Finally (after reading your post) I see it is generating partial charges for piroxicam. But there is a problem. The molecule has only one charge group (a group of atoms having integral charge ). I don't know whether it is reasonable. I expected more charge groups (e.g. carbonyl group).
ATB server has also generated partial charges for my molecule. I thought partial charges assigned by antechamber would be better. I have actually used the optimized geometry of ATB server as an input to antechamber (ACPYPE). May be I should use partial charges assigned by ATB server. Thanks.
DEAR Uttam,
i suggest Gaussian resp charge to calculate partial charges .its more accurate because of quantum calculation nature.also antechamber is more familiar with Gaussian output file.
for more information contact me with this email :
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