Urszula,
I looked at your SUN_am.moL2; the charges look... terrible; no charge
equivalencing at all even between the hydrogen of the methyl groups!?
I just hope there is an option to make the charges for these methyl
hydrogens equivalent...
Moreover, you computed the charges for a modified serine with a
NH2-group and a aldehyde-group for the peptide backbone; you will not
be able to include this molecule within the backbone of your protein:
in your case you need a central fragment.
You could follow the following strategy by using R.E.D. Server:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
or from a single P2N file
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
in your case the side chain of your dipeptide would consist in the
side chain of a serine with this covalently linked nerve agent to serine
if the conformation you get after geometry optimization does not look
reasonable (i.e. different to that you expect) you could split the
Serine dipeptide and the linked nerve agent into two different
building blocks (BD); in this case, you will have to define an
additional inter-molecular charge constraint between these 2 BD.
regards, Francois
> I was trying to get the parameters for my covalently linked nerve
> agent to serine 203,
> SUN.mol2, I run simple antechamber and parmcheck, but after loading
> them to leaps
> I am getting parameters errors ..
>
> inside my parmcheck file is:
>
>
> remark goes here
> MASS
>
> BOND
>
> ANGLE
>
> DIHE
>
> IMPROPER
> c3-h4-c -o 10.5 180.0 2.0 General
> improper torsional angle (2 general atom types)
>
> NONBON
>
> after reading into leap ...
>
> FATAL: Atom .R<SUN 203>.A<N 1> does not have a type.
> FATAL: Atom .R<SUN 203>.A<CA 2> does not have a type.
> FATAL: Atom .R<SUN 203>.A<CB 3> does not have a type.
> FATAL: Atom .R<SUN 203>.A<OG 4> does not have a type.
> FATAL: Atom .R<SUN 203>.A<C 5> does not have a type.
> FATAL: Atom .R<SUN 203>.A<O 6> does not have a type.
> FATAL: Atom .R<SUN 203>.A<O1 7> does not have a type.
> FATAL: Atom .R<SUN 203>.A<P1 8> does not have a type.
> FATAL: Atom .R<SUN 203>.A<N1 9> does not have a type.
> FATAL: Atom .R<SUN 203>.A<C2 10> does not have a type.
> FATAL: Atom .R<SUN 203>.A<C1 11> does not have a type.
> FATAL: Atom .R<SUN 203>.A<O2 12> does not have a type.
> FATAL: Atom .R<SUN 203>.A<C3 13> does not have a type.
> FATAL: Atom .R<SUN 203>.A<C4 14> does not have a type.
>
> I was thinking about using the RED program but I am not quite sure how
> to prepare the right pdb file ... Could someone help me with this?
>
> /Urszula
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Received on Fri Dec 09 2011 - 05:30:04 PST
