AMBER Archive (2007)

Subject: Re: AMBER: Problems loading parameter file in tleap

From: Eddie Men (pckboy_at_gmail.com)
Date: Fri Sep 21 2007 - 06:27:35 CDT

I have noticed this problem is old

I just have no idea how "safe" is the probably line
+--- Sp0 probably means a new atom type is involved

Someone a couple of years back even suggested to ignore the problem
http://structbio.vanderbilt.edu/archives/amber-archive/2005/1775.php

Any word of warning before I keep going with a failed 1000 hours
molecular simulation?.
 

Eddie

 
> Greetings Amber users.
>
> I have this interesting not quite welcome issue:
> when I load my parameter file and the pdb file the following output
> appears:
>
> CMPLX=loadPdb AQUI.pdb
> Loading PDB file: ./AQUI.pdb
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-C1-C2-*
> +--- With Sp0 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> total atoms in file: 6
> > check CMPLX
> Checking 'CMPLX'....
> WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
> Checking parameters for unit 'CMPLX'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Warnings: 1
> Unit is OK.
> > quit
>
>
>
> The unit however is okay. Any ideas?.
>
> I am doing Oxalate, and yes, the charge is supposed to be -2.
> Should I try to combine atom types in a different fashion?.
> Carbons are C1, Oxygens are O2 type
>
> Thanks for the input!
>
> Eddie
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu