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Frequent Asked Questions about ACPYPE

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Alan edited this page Jun 1, 2020 · 1 revision

FAQ

  • Q: What are ACPYPE limitations?
  • A: Because ACPYPE is based on Antechamber, it will as well inherit some of its limitations like not being possible to work with organic molecule with open valences; containing others atoms than C, N, O, S, P, H, F, Cl, Br and I; or covalently bonded to another molecule. If one wants parameters for a modified amino acid residue, one way of getting it is by neutralising the N- and C- termini and then fit manually the additional parameters to the modified residue (See more about it in questions below).

Ideally, one should know well about the molecule one is trying to parametrise and should read the pertinent papers related to the force field intended to be used (see references below). Therefore be warned if using ACPYPE/Antechamber as a blackbox.

  • Q: How do I install ACPYPE?

  • A: Please, read How To Use ACPYPE wiki page.

  • Q: Why only one residue per try?

  • A: ACPYPE is not ready to deal with more than one chain. In fact, antechamber will likely take the first residue name and apply it for all. Results can be completely unpredictable. Split your molecular system with one ligand only in each pdb/mol2 file.

  • Q: I have a modified residue in my protein or ligand covalently bonded to my protein and ACPYPE doesn't work. Why?

  • A: ACPYPE is not that smart to automatise this procedure, but one can still obtain a topology. You need to isolate your special residue with the 2 next residues it is connected: Res1-MY_RES-Res2 and then make those Res1 and Res2 (N and T) zwitterions and run ACPYPE. Once you have the parameters in hand, you'll need to manually tweak your topology data around the bonds connected to the modified residue.

  • Q: Why this error /bin/sh: -i: not found"?

  • A: You haven't setup you $AMBERHOME and $PATH properly. Rerun ACPYPE with -d option for more info.

  • Q: amb2gmx.pl doesn't use antechamber and needs only parmtop and inpcrd files. Why acpype cannot reproduce amb2gmx.pl completely?

  • A: Not yet! In fact, this feature is on progress. Once done, one will be able to use tleap/sleap/xleap from AMBER package to generate parmtop and inpcrd files and use them to generate GROMACS files via acpype, in the way amb2gmx.pl does, with no need of ffAMBER.

    • DONE!

  • Q: Why acpype fails saying it cannot found antechamber?

  • A: If you're not using ACPYPE as a replacement for amb2gmx.pl (see the strikeout question above), then you must have antechamber installed and properly set: either via $AMBERHOME environment variable or with the path to folder containing antechamber binary in your $PATH.

  • Q: I downloaded a pdb file from PDB and it seems to not have hydrogens. When I use acpype it fails, why?

  • A: You definitely need a pdb/mol2 input file with all atoms (including hydrogens), otherwise antechamber (including a step with mopac) will not know or (even worse) will calculate wrong parameters and charges. You can use either, e.g., babel -h _mol_w/o_H_.pdb _mol_with_H.pdb or YASARA View to automatically add missing hydrogens to your compound. The former just puts 'H' for atom names while the latter puts more meaningful atom name, e.g., 'HCA' for a H bonded to a CA and not a simply 'H' as babel does.

  • Q: My complex has 2 ligands, what can I do to get it working with GROMACS?

  • A: Let's say you have lig1 and lig2. Once you have used ACPYPE for each ligand, you need to merge the [ atomtypes ] fields, i.e., take the atoms lines from [ atomtypes ] of lig2.itp (delete field [ atomtypes ] and its content in lig2.itp file) and add the atoms lines that are not already there in [ atomtypes ] of lig1.itp. Then in your Complex.top file insert line #include "lig1.itp", and in the line below, #include "lig2.itp" all right below line #include "ffamber*.itp". This procedure applies always you have n >= 2 ligands.

  • Q: When I'm trying to simulate systems with protonated ADP/ATP states, whose topologies were generated by ACPYPE, I usually get that one of the protons linked to the hydroxyl group of phosphates moving too much towards to the oxygen or phosphorus, like if there was no van der Waals repulsion between them?

  • A: This happens due to the strong Coulomb force of attraction between the atoms involved, since they have opposite charges, and the total absence of VDW radii parameters. To solve it, please do this in your *.itp file:

Replace line:

# For GAFF
ho       ho          0.00000  0.00000   A     0.00000e+00   0.00000e+00 ; 0.00  0.0000

# For AMBER
HO       HO          0.00000  0.00000   A     0.00000e+00   0.00000e+00 ; 0.00  0.0000

with

# For GAFF
ho       ho          0.00000  0.00000   A     1.06908e-01   6.56888e-02 ; 0.00  0.0000

# For AMBER
HO       HO          0.00000  0.00000   A     1.06908e-01   6.56888e-02 ; 0.00  0.0000
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