Parameter files are updated for RNA/DNA calculation

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lli5
Posts: 38
Joined: Thu Sep 22, 2011 8:44 am

Parameter files are updated for RNA/DNA calculation

Post by lli5 » Thu Nov 03, 2011 10:39 am

Dear DelPhi Users,

The parameter files (crg and siz files) were updated to include parameters
for nucleic acids (RNA and DNA). It was done for Amber, Charmm and Parse
force field. Soon it will be done for OPLS as well. We attempted to make
these files less sensitive to the particular algorithm protonating
RNA/DNA, but be aware that there will be always exceptions. Typical
example are the names of hydrogens, which some algorithms assign as H5'2,
while others as H5''. Be advised to check Delphi output for WARNINGs of
non-integer charges and manually fix the names in the "crg" and "siz"
files. Let's us know so we can add in the distribution these variations of
atomic names.

For delphi development team, Lin Li

clive
Posts: 1
Joined: Wed Jun 13, 2018 2:58 pm

Re: Parameter files are updated for RNA/DNA calculation

Post by clive » Wed Jun 13, 2018 2:58 pm

lli5 wrote:
Thu Nov 03, 2011 10:39 am
Dear DelPhi Users,

The parameter files (crg and siz files) were updated to include parameters
for nucleic acids (RNA and DNA). It was done for Amber, Charmm and Parse
force field. Soon it will be done for OPLS as well. We attempted to make
these files less sensitive to the particular algorithm protonating
RNA/DNA, but be aware that there will be always exceptions. Typical
example are the names of hydrogens, which some algorithms assign as H5'2,
while others as H5''. Be advised to check Delphi output for WARNINGs of
non-integer charges and manually fix the names in the "crg" and "siz"
files. Let's us know so we can add in the distribution these variations of
atomic names.

For delphi development team, Lin Li
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JosephDixon
Posts: 1
Joined: Mon Jun 18, 2018 4:24 am

Re: Parameter files are updated for RNA/DNA calculation

Post by JosephDixon » Mon Jun 18, 2018 4:25 am

We attempted to make these files less sensitive to the particular algorithm protonating RNA/DNA, but be aware that there will be always exceptions. Typical example are the names of hydrogens, which some algorithms assign as H5'2, while others as H5''. Be advised to check Delphi output for WARNINGs of non-integer.

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