Hi Dac,
I followed last suggested steps.I tried R.E.D tutorial (Tutorial: the mol3 file format)
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Tutorial: the mol3 file format
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I followed these steps:> HAR = loadmol2 HAR.mol2Loading Mol2 file: ./HAR.mol2Reading MOLECULE named HAR> loadAmberParams HAR.frcmodLoading parameters: ./HAR.frcmodReading force field modification type file (frcmod)Reading title:Remark line goes here> 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 frcmod14SBparm10> aa = sequence {ACE HAR NME}Sequence: ACESequence: HAR
Warning: One sided connection. Residue (HAR) missing connect0 atom.Sequence: NME
Warning: One sided connection. Residue (ACE) missing connect1 atom.> set HAR head HAR.1.N> set HAR tail HAR.1.C> set HAR.1 connect0 HAR.1.N> set HAR.1 connect1 HAR.1.C> set HAR head HAR.1.N> set HAR tail HAR.1.C> set HAR.1 connect0 HAR.1.N> set HAR.1 connect1 HAR.1.C> ACE = loadmol2 ACE.mol2Loading Mol2 file: ./ACE.mol2Reading MOLECULE named ACE> NME = loadmol2 NME.mol2Loading Mol2 file: ./NME.mol2Reading MOLECULE named NME> set ACE tail ACE.1.C> set ACE.1 connect1 ACE.1.C> set NME head NME.1.N> set NME.1 connect0 NME.1.N> savepdb aa aa-new.pdbWriting pdb file: aa-new.pdb> desc aaUNIT name: ACEHead atom: nullTail atom: nullContents:R<ACE 1>R<HAR 2>R<NME 3>> saveoff aa aa.off Creating aa.offSaving aa.Building topology.Building atom parameters.> saveamberparm aa aa.prmtop aa.inpcrdChecking Unit.Building topology.Building atom parameters.Building bond parameters.Building angle parameters.Building proper torsion parameters.Building improper torsion parameters. total 2 improper torsions appliedBuilding H-Bond parameters.Incorporating Non-Bonded adjustments.Not Marking per-residue atom chain types.Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked:
res total affected
HAR 1 ) (no restraints)> quit Quit
Exiting LEaP: Errors = 0; Warnings = 2; Notes = 0. But I am not sure, is this the right way to do for connect atoms. Also PDB (attached) looks weird.
Thanks,Sarah
On Monday, 7 September 2020, 16:58:00 BST, David A Case <david.case.rutgers.edu> wrote:
On Mon, Sep 07, 2020, Sarah Jane wrote:
>> HAR = sequence {ACE HAR NME}
Again, don't reuse the idenifier "HAR". Just type something like:
x = sequence {ACE HAR NME}
Now the simplest thing to do is to use the bond command to add any
missing bonds. If you are going to be using the HAR residue a lot, you
could use tleap to set the connect0 and connect1 atoms to the N and C
atoms of the HAR residue (then use saveOff to save this as an off file
for use later.) But try the simpler thing first.
After you create a prmtop file, use parmed to ensure that you have the
bonds you want.
....dac
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Received on Wed Sep 09 2020 - 05:30:04 PDT
