Re: [AMBER] Fw: covalent molecule and modified residue parameters

From: Sarah Jane <>
Date: Thu, 3 Sep 2020 15:21:03 +0000 (UTC)

 Hi Dac,
I did the suggested changes and tried capping using this command but got the following error.
> loadmol2 HAR.mol2Loading Mol2 file: ./HAR.mol2Reading MOLECULE named UNK> loadAmberParams HAR.frcmodLoading parameters: ./HAR.frcmodReading force field modification type file (frcmod)Reading title:Remark line goes here> saveOff HAR HAR.lib> loadOff HAR.libLoading library: ./HAR.lib> listACE       ALA       ARG       ASH       ASN       ASP       CALA      CARGCASN      CASP      CCYS      CCYX      CGLN      CGLU      CGLY      CHIDCHIE      CHIP      CHIS      CHYP      CILE      CLEU      CLYS      CMETCPHE      CPRO      CSER      CTHR      CTRP      CTYR      CVAL      CYMCYS       CYX       GLH       GLN       GLU       GLY       HAR       HIDHIE       HIP       HIS       HYP       ILE       LEU       LYN       LYSMET       NALA      NARG      NASN      NASP      NCYS      NCYX      NGLNNGLU      NGLY      NHE       NHID      NHIE      NHIP      NHIS      NILENLEU      NLYS      NME       NMET      NPHE      NPRO      NSER      NTHRNTRP      NTYR      NVAL      PHE       PRO       SER       THR       TRPTYR       VAL       frcmod14SBgaff      parm10> seq = sequence {ACE HAR NHE}
Error: sequence: Illegal UNIT named: HAR

    On Friday, 28 August 2020, 02:03:37 BST, David A Case <> wrote:
 On Thu, Aug 27, 2020, Sarah Jane wrote:
>  Here is the antechamber command:antechamber -fi pdb -i HAR.pdb -fo mol2 -o
>  HAR.mol2 -c bcc -nc 0 -at amber -s 2 -dr no

You HAR.pdb file has a very bad placement of the HO1 atom: it is only
1.6 Å from the CZ atom.  I'm guessing that this is confusing to
antechamber, although the C=N double bond *could* be a problem.

Try rotating the HO1 above to point away from the rest of the molecule.

You also have mulitple unsatisfied valencies at the C and N atoms:
antechamber expects a complete moledule, not just an amino acid
fragment.  You need to put capping groups on, run antehcamber, then take
the capping groups off. 

Try this: go to, click on "tutorials and
examples", then on "generate residue topology files for non-standard
amino acids".  (Apologies if you have already done this.....)

...good luck...dac

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Received on Thu Sep 03 2020 - 08:30:03 PDT
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