[gmx-users] Re: Problem with Amber99SB-ILDN ff

[Alan]

Hi

I can't see which commands you typed. Your second try "/bin/sh: 1: -i: not
found" means that you $PATH is not properly setup for Amber Tools. And if
you using open babel, it has to be your $PATH as well.

For the first case, it's all about which structure you were trying to run.
>From the pdbs you sent me, none of them are correct. The test.pdb is not in
a zwitterionic form and ACPYPE can only work with one residue only,
so op-glu2.pdb is not OK either.

Nevertheless, the error messages ACPYPE printed are re ANTECHAMBER, and
once we cleared your structure, you'd better ask at AMBER list for this
issues. But bear in mind that 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 of the 2
adjacent residues (so make a tripeptide) and then fit manually the
additional parameters to the modified residue.

Alan


On 17 July 2013 14:30, Melchor S. <msmqbm at cid.csic.es> wrote:

> Hi again,
> I can give more details about acpype error. This is the error that I
> obtained,
>
>
> ===============================================================================================
> | ACPYPE: AnteChamber PYthon Parser interfacE v. 2012-09-13 14:55:47Z Rev:
> 389 (c) 2012 AWSdS |
>
> ===============================================================================================
> ==> ... charge set to 0
> ==> ... converting pdb input file to mol2 input file
> ==> * Babel OK *
> ==> Executing Antechamber...
>
> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> 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 PSCUTOFF in define.h and recompile bondtype.c
>     Be cautious, use a large value of PSCUTOFF (>100) will significantly
> increase the computation time
> Running: /home/melchor/Software/amber12/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Running: /home/melchor/Software/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0
> -o ANTECHAMBER_AC.AC -p gaff
> Total number of electrons: 61; net charge: 0
> INFO: Number of electrons is odd: 61
>       Please check the total charge (-nc flag) and spin multiplicity (-m
> flag)
>
> Running: /home/melchor/Software/amber12/bin/sqm -O -i sqm.in -o sqm.out
> Error: cannot run "/home/melchor/Software/amber12/bin/sqm -O -i sqm.in -o
> sqm.out" of bcc() in charge.c properly, exit
>
>
> ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ERROR: Antechamber failed
>
> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> /bin/sh: 1: -i: not found
>
> ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ERROR: Parmchk failed
> ERROR: Tleap failed
> ==> ... trying Sleap
> ==> Executing Sleap...
>
> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> /bin/sh: 1: -f: not found
>
>
> ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ERROR: Sleap failed
> ==> Removing temporary files...
> ACPYPE FAILED: [Errno 2] No such file or directory: 'test_AC.prmtop'
>
> So I thought that maybe the problem was my structure but even if I try this
> tutorial :
> http://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs, I obtain a
> similar error:
>
>
> ===============================================================================================
> | ACPYPE: AnteChamber PYthon Parser interfacE v. 2012-09-13 14:55:47Z Rev:
> 389 (c) 2012 AWSdS |
>
> ===============================================================================================
> ==> ... charge set to 0
> ==> ... converting pdb input file to mol2 input file
> ==> * Babel OK *
> ==> Executing Antechamber...
> ==> * Antechamber OK *
>
> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> /bin/sh: 1: -i: not found
>
> ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ERROR: Parmchk failed
> ERROR: Tleap failed
> ==> ... trying Sleap
> ==> Executing Sleap...
>
> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> /bin/sh: 1: -f: not found
>
>
> ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ERROR: Sleap failed
> ==> Removing temporary files...
> ACPYPE FAILED: [Errno 2] No such file or directory: 'Ligand_AC.prmtop'
> Total time of execution: 13m 3s
>
> Someone could help me? Is something about the configuration ?
>
> Thanks in advance,
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Problem-with-Amber99SB-ILDN-ff-tp5009641p5009926.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588