The N terminal has multiple Hydrogens (H2 and H3) attached to Nitrogen
instead of just the H. Rename each of the H atoms to H2 or H3 or delete and
let tleap build them in. The OXT atom is the extra oxygen in the COO at the
C terminal. If you don't want your terminal residues converted, you should
block them or edit the leaprc file.
On 6/12/07, Taryn Hartley <taryn_hartley.hotmail.com> wrote:
>
> 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.pdb
>
> Created 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 templates
>
> Then 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 parameters
> Parameter 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 -0400
> From: carlos.simmerling.gmail.com
> To: amber.scripps.edu
> Subject: 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* <taryn_hartley.hotmail.com > 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,
>
> Taryn
>
>
> ------------------------------
> Discover the new Windows Vista Learn more!<http://search.msn.com/results.aspx?q=windows+vista&mkt=en-US&form=QBRE>
>
>
>
>
>
> ------------------------------
> Invite your mail contacts to join your friends list with Windows Live
> Spaces. It's easy! Try it!<http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jun 13 2007 - 06:07:34 PDT
