AMBER Archive (2007)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Sep 21 2007 - 06:55:39 CDT

Quoting Eduardo Mendez <pckboy_at_gmail.com>:

> 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?.

Yes, I got this type of problem also. It appends because you forgot to
define a new atom type, or because a leap command arrives after
(instead of before) another one...

See below the script, it worked for me (no error message):
--------------------------------------
source leaprc.glycam04 # or any other force field
addAtomTypes {
         { "CA" "C" "sp3" }
         { "HA" "H" "sp3" }
}
FRCMOD = loadamberparams frcmod.cd
--------------------------------------
On the contrary, with the 2nd script below, I get a similar error than
the one you reported:
--------------------------------------
source leaprc.glycam04 # or any other force field
FRCMOD = loadamberparams frcmod.cd
addAtomTypes {
         { "CA" "C" "sp3" }
         { "HA" "H" "sp3" }
}
--------------------------------------

regards, Francois

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