[AMBER] Adding a new atom type - ATTN, no polarizability parameter

From: Henrik Hariman <henrik.hariman.gmail.com>
Date: Tue, 27 Feb 2018 15:21:59 -0500

Dear all,

I need to have a new atom type called c4 (c4 is supposed to be identical to
the available c3 except their name). By recommendation of parmchk2 I added
a new atom type to the PARMCHK.DAT file. To do so, I simply copied the
lines which contain c3 and just changed the c3 to c4 in the pasted lines,
so that I have now both c3 and c4 in my PARMCHK.DAT file.

Now, the ``parmchk2 -i case.mol2 -o case.frcmod -f mol2 -a Y'' gives me a
case.frcmod with the c4 as a new atom type (which is fine) as below:

MASS
c3 12.010 0.878
hc 1.008 0.135
ca 12.010 0.360
.
.
c4 12.010 0.000 ATTN, no polarizability parameter

As you see the c4 shows up in a fashion as the above last line, also, in
other sections wherever the c4 in involved I have something like below for
example:

hc-c4-hc 0.000 0.000 ATTN, need revision

I even did the same for the all files located in
``amber16/dat/antechamber'' whichever has c3.

The parmchk2.c file in antechamber has some lines which output the above
massages (ATTN, ...), but I could not figure it out, so, would you please
let me know how to add a c4 atom type with identical information as c3
except the name?

Thanks.

Cheers,
Henrik Hariman
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Received on Tue Feb 27 2018 - 12:30:04 PST
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