On Sun, Mar 30, 2025, Rahul Singal via AMBER wrote:
>I am currently modeling a DNA system incorporating TCO and TCNitro FRET
>probes. I initially used Antechamber to generate the parameters for the
>probes, but I recently realized that I should have used parmcal to compute
>the bond and angle parameters using GAFF2 (as provided in the gaff2.dat
>file in AmberTools23).
>While I was able to calculate most parameters, I couldn't find the torsion parameters for the following dihedrals:
>
> *
>h1–c3–o–P
> *
>c3–c3–o–P
> *
>c3–o–P–O2
> *
>c3–o–P–OS
>
First: remember that upper case atom types come from Amber, whereas lower
case types are for GAFF2. So, you have to figure out how to translate lower
case atom types (in gaff2) to their upper case equivalents.
Examples: a phosphorus atom in a phosphate group is P in Amber but p5 in
gaff2 (since p5 corresponds to phosphorus with four connected atoms). O2 in
Amber is an oxygen with one connected atom, and becomes o in gaff2. OS in
Amber becomes os in gaff2. etc. [Look in $AMBERHOME/dat/leap/parm/gaff2.dat
to find explanations for gaff2 atom types.]
But you seem to have a problem I can't resolve without more information: you
seem to have "o" as the atom type between c3 and P, but "o" in gaff2 is for an
oxygen with only one connected atom. This almost certainly should be "os",
but it's unclear what the origin of this problem is.
...hope this helps....dac
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Received on Mon Mar 31 2025 - 13:00:03 PDT
