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 - 10:00:02 PDT
