Dear Dac,
Thank you for the help.
On Sun, Sep 16, 2012 at 12:35 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Sat, Sep 15, 2012, Shomesankar Bhunia wrote:
>
> > I am trying to create topology and coordinate file for
> raloxifene-protein
> > complex. I have generated the paramtop and inpcrd files for the ligand as
> > well as generated a ral.lib. But when I am typing the script
> "*saveamberparm
> > complex 1ERR_A.prmtop 1ERR_A.inpcrd*" it is returning the error as
> > mentioned below the tleap.in script.What next? Thanks in advance.
> >
> > source leaprc.ff99SB
> > source leaprc.gaff
> > loadamberparams ral.frcmod
> > loadoff ral.lib
> > complex = loadpdb 1ERR_A.pdb
> > saveamberparm complex 1ERR_A.prmtop 1ERR_A.inpcrd
> > savepdb complex 1ERR_A.pdb
> >
> >
> > FATAL: Atom .R<PRO 518>.A<HG1 17> does not have a type.
> > FATAL: Atom .R<PRO 518>.A<HD1 18> does not have a type.
> > FATAL: Atom .R<LEU 519>.A<HN 20> does not have a type.
> > FATAL: Atom .R<LEU 519>.A<HB1 21> does not have a type.
>
> The atom names in your PDB file don't match those in the Amber libraries.
> Amber uses the current PDB standard (version 3.x), which in turn follows
> IUPAC standards. Your input pdb file has hydrogen names that follow some
> mixed scheme.
>
> One common option is to remove the hydrogen atoms from the input pdb file,
> and
> let LEaP rebuild them and give them appopriate names. There are also
> programs
> available (at PDB sites and elsewhere) that will convert old format files
> to
> new ones (although your input file doesn't appear to follow any particular
> format: "HB1", "HG1", etc. look like pdb format 2.x, but "HN" does not.)
>
> ...good luck...dac
>
> [Aside: you are just asking for trouble if you use the same file name for
> the "loadpdb" command as for the "savepdb" command. This is likely to
> cause
> confusion, and keep you from re-running the calculations later.]
>
>
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Received on Sun Sep 16 2012 - 21:30:04 PDT
