Re: [AMBER] parmchk2 frcmod file

From: David A Case <david.case.rutgers.edu>
Date: Fri, 26 Oct 2018 08:30:45 -0400

On Fri, Oct 26, 2018, Jon Uranga wrote:
>
> I am writing with regard to creating a non standard amino acid residue
> (Acetylated lysine, ACK). I am following the B5 tutorial and everything is
> working well for me, except from the last step, which involves creating the
> frcmod file.
>
> A segmentation fault comes as a result, when executing parmchk2 and I have
> observed that this has also occurred to other users before. I am using
> AMBER14, but have also tested AMBER18, just in case. In this last case when
> executing parmchk2 the error message is more detailed saying:
>
> Warning: Atom type (CX) is not in PARMCHK.DAT; using default values
> for improper_flag [0], group_id [0], and equivalent_flag [0].
> Warning: No mass information for atom type (CX); set to 0.0.
> It is recommended to add the new atom type (CX) to PARMCHK.DAT.

Thanks for the report. The parmchk2 program should certainly not be
giving a segfault. However, it would be very helpful to know exactly
what options you gave to parmchk2. You should have something like
"... -p $AMBERHOME/dat/leap/parm/parm10.dat -pf 1". Much of the
behavior you report might be expected if you didn't have this.

Here's what I tried:

In PARMCHK.DAT, I made these changes:

godel% git diff PARMCHK.DAT
diff --git a/dat/antechamber/PARMCHK.DAT b/dat/antechamber/PARMCHK.DAT
index d14a9fa064..a6b8ba690e 100644
--- a/dat/antechamber/PARMCHK.DAT
+++ b/dat/antechamber/PARMCHK.DAT
.@ -205,6 +205,9 @@ CORR cf 2.5 11.2 3.8 2.2 3.0 1.9 9.2 -1.0 19.2
 PARM CT 0 0 12.01 0 6
 EQUA c3
 #
+PARM CX 0 0 12.01 0 6
+EQUA c3
+#
 PARM CV 1 0 12.01 0 6
 EQUA cc
 EQUA cd

Then "parmchk2 -i ack.prepi -f prepi -o dac.frcmod -p
$AMBERHOME/dat/leap/parm/parm10.dat -pf 1" went fine, with no segfault.


> CT-O 0.00 0.000 ATTN, need revision
> C -O -CT 0.000 0.000 ATTN, need revision
> HC-CT-O 0.000 0.000 ATTN, need revision
> C -CT-O 0.000 0.000 ATTN, need revision
> HC-CT-O -C 1 0.000 0.000 0.000 ATTN, need
> revision
> C -CT-O -C 1 0.000 0.000 0.000 ATTN, need
> revision

I get the same missing parameters. Have you tried to make a prmtop file
without using the frcmod file that parmchk2 creates?

(cc-ing to junmei, since I don't immediately see what is going on here.)

...thx...dac


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 26 2018 - 06:00:05 PDT
Custom Search