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
Thanks,Sarah
On Friday, 28 August 2020, 02:03:37 BST, David A Case <david.case.rutgers.edu> 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 http://ambermd.org/antechamber/, 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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- application/octet-stream attachment: HAR.mol2
Received on Thu Sep 03 2020 - 08:30:03 PDT
