Hi,
just to add, more simpler thing you can do is this.
you need atom hybridisations defined. e.g. say you are using amber10 (and assuming you need to define atom types from ff03) or if NOT you can define new atomtypes and also hybridisations in file described below.
So lets say in $AMBERHOME/amber10/dat/leap/cmd/leaprc.ff03. you will see all atoms are defined defined. You can source this file commenting out (using #) undesired *.frcmod and *.dat that you dont want to load.
.
.
.
addAtomTypes {
{ "H" "H" "sp3" }
{ "HO" "H" "sp3" }
.
.
.
#parm99 = loadamberparams parm99.dat (I am using # sign to not to load, assuming your tys.frcmod has all params.)
sourcing this file having addAtomTypes will not show warnings.
________________________________
From: FyD <fyd.q4md-forcefieldtools.org>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Friday, July 13, 2012 12:33 PM
Subject: Re: [AMBER] Sulfotyrosine force field
Dear Pedro,
We get often this type of errors and for sure we always try to avoid
these messages. t/xLEaP works well when you control what you do... and
is quite buggy in 'some' "other" circumstances...
I think your problem (common) is related to atom type definition.
Check that all your atom types are defined (and defined before you
load your frcmod file). See the "addAtomTypes" command in LEaP. Check
also that the vdW params are well defined for the new atom types you
have introduced in your frcmod file...
More generally, always look at error messages and warning messages
printed by LEaP: this is a good way to avoid many primary problems...
regards, Francois
> I have a problem with created non-standard amino acids, Sulfotyrosine. I
> created the force field for this sulfotyrosine (tys.frcmod and tys.lib)
> using the "RESP ESP charge Derive Server", then using antechamber. However
> when I load a sulfotyrosine pdb in tleap I got the following error, please
> see below. Can someone tell me how to fix it or I can ignore it?
>
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-S-O3-*
> +--- With Sp0 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-CE2-CD2-*
> +--- With Sp0 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-OH-S-*
> +--- With Sp0 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> ................................................. similar errors
> below...............................................
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Received on Fri Jul 13 2012 - 00:30:03 PDT
