On Wed, Sep 9, 2015 at 11:17 AM, Arjun Sharma <arjunsharma83.gmail.com>
wrote:
> Dear Jason,
>
> When you assign syn- and anti- position to carboxylates do you specify it
> as dummy atoms (zero charge and zero VDWs) with coordinate positions in
> mol2 file ? I assigned same bond length O-H (0.96) and same angle between
> H-O-H (120).
>
> C -3.3040 1.1729 -1.0796 C 0.520
> O -2.4523 0.5812 -1.9611 O -0.440
> O -2.8408 1.8405 0.0123 O -0.530
> H -1.8963 1.9010 0.1730 H 0.450
> H -1.7567 1.6750 0.1566 H 0.000
> H -1.6838 0.9879 0.1524 H 0.000
> H -1.7867 1.5643 0.1657 H 0.000
>
> I can successfully generate the cpin file (explicit CpHMD). But when I
> use the new topology file generated with the Cpin file for minimization ,
> it crashes with really high bond energy and EEL. What am I doing wrong ? I
> would really appreciate your help.
>
​Did you define bonds between the oxygen and each hydrogen? Use ParmEd
(and printBonds) to make sure that the bonds you *intended* to add were
really added.
It's really impossible to determine the error here given just this
information.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 09 2015 - 09:00:05 PDT
