RE: AMBER: Atom types

From: Taryn Hartley <>
Date: Tue, 12 Jun 2007 11:25:30 -0600

This is the message I get when I enter the "loadpdb command". I used leaprc.ff99SB (at Mr. Simmerling's suggestion). This is what it said:Loading PDB file: ./cluster7.pdbCreated a new atom named: H within residue: .R<NPHE 1> Added missing heavy atom: .R<CILE 20>.A(OXT 20>Created a new atom named: H within residue: .R<NPHE 21> Added missing heavy atom: .R<CILE 40>.A(OXT 20> Created a new atom named: H within residue: .R<NPHE 41> Added missing heavy atom: .R<CILE 60>.A(OXT 20> total atoms in file: 564 Leap added 480 missing atoms according to residue templates: 3 Heavy 477 H / lone pairs The file contained 3 atoms no in residue templatesThen when I went to save the .inpcrd and prmtop files, this is the message I got:Checking Unit.WARNING: The unperturbed charge of the unit: 3.000000 is not zero.FATAL: Atom .R<NPHE 1>.A<H 23> does not have a type.FATAL: Atom .R<NPHE 21>.A<H 23> does not have a type.FATAL: Atom .R<NPHE 41>.A<H 23> does not have a type.Failed to generate parametersParameter file was not saved.This molecule has only amino acids, and is directly from the Protein Data Bank with no modifications made. I have also tried with the Human Prion molecule from the protein data bank and got similar readouts. Is this a common hang-up with using PDB files or am I doing something wrong? - Taryn Hartley Date: Fri, 8 Jun 2007 14:47:43 -0400From: amber.scripps.eduSubject: Re: AMBER: welcome to Amber!1) don't use parm99 unless you are sure you want all of its problems.I recommend ff99SB, check the archives for details.2) copy error messages in the email so we can see the problem. does the protein have anything other than amino acids?On 6/8/07, Taryn Hartley < > wrote: I am a new-to-Amber user and after completing the tutorials, am attempting to work with some molecules pertaining to my research. In loading and attempting to save .inpcrd and .prmtop files using xLeap (with force field 99, leaprc.ff99) I am recieving "FATAL" error messages, saying that some of my atoms don't have atom types. The molecules I am using are directly from the Protein Data Bank with no modifications. Has anyone else confronted this problem? If so, what solution did you find works best? Thanks in advance, TarynDiscover the new Windows Vista Learn more!
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Received on Wed Jun 13 2007 - 06:07:33 PDT
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