Re: [AMBER] parmchk2 frcmod file

From: Jon Uranga <jonur9.gmail.com>
Date: Fri, 26 Oct 2018 14:57:34 +0200

Many thanks for your email.

I made an error, preparing the mc file. Basically, those connections came
due to the fact that I did not set up properly that file. Herein, I post
the correct one:

HEAD_NAME N2
TAIL_NAME C8
MAIN_CHAIN C7
OMIT_NAME H15
OMIT_NAME H16
PRE_HEAD_TYPE C
POST_TAIL_TYPE N
CHARGE 0.0

And the prepi file looks different from the one posted before:

    0 0 2

This is a remark line
molecule.res
ACK INT 0
CORRECT OMIT DU BEG
  0.0000
   1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
   2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
   3 DUMM DU M 2 1 0 1.523 111.21 .0 .00000
   4 N2 N M 3 2 1 1.540 111.208 -180.000 -1.023070
   5 H14 H E 4 3 2 1.019 38.395 -67.039 0.411990
   6 C7 CX M 4 3 2 1.456 110.007 -168.230 0.505248
   7 C6 CT 3 6 4 3 1.547 111.272 -146.729 -0.039565
   8 C5 CT 3 7 6 4 1.516 113.400 -54.995 -0.018750
   9 C4 CT 3 8 7 6 1.551 110.064 -166.019 -0.032437
  10 C3 CT 3 9 8 7 1.528 111.039 168.069 -0.161996
  11 N1 N B 10 9 8 1.458 110.078 -177.270 -0.623260
  12 C2 C B 11 10 9 1.335 124.072 79.476 0.856166
  13 C1 CT 3 12 11 10 1.509 117.554 -179.446 -0.390005
  14 H1 HC E 13 12 11 1.101 115.057 -5.880 0.117754
  15 H2 HC E 13 12 11 1.101 108.249 116.230 0.117754
  16 H3 HC E 13 12 11 1.100 108.168 -128.206 0.117754
  17 O1 O E 12 11 10 1.239 123.377 -1.037 -0.585333
  18 H4 H E 11 10 9 1.013 117.634 -99.492 0.391979
  19 H5 HP E 10 9 8 1.102 111.828 61.840 0.144740
  20 H6 HP E 10 9 8 1.101 109.619 -58.340 0.144740
  21 H7 HC E 9 8 7 1.101 109.676 49.548 0.060798
  22 H8 HC E 9 8 7 1.103 110.699 -69.045 0.060798
  23 H9 HC E 8 7 6 1.102 111.062 70.284 0.025229
  24 H10 HC E 8 7 6 1.105 109.485 -46.564 0.025229
  25 H11 HC E 7 6 4 1.102 107.503 -177.588 0.016237
  26 H12 HC E 7 6 4 1.104 108.745 68.966 0.016237
  27 H13 H1 E 6 4 3 1.109 107.030 95.404 -0.006915
  28 C8 C M 6 4 3 1.503 111.177 -20.855 0.319291
  29 O2 O E 28 6 4 1.240 122.727 -127.903 -0.450617


LOOP

IMPROPER
   C2 C3 N1 H4
   C1 N1 C2 O1
   C7 +M C8 O2

DONE
STOP

Then, adding the 3 lines, you posted, to PARMCHK.DAT solves the problem
with C_alpha atom type.

Many thanks for your time and consideration.

Best regards,

Jon Uranga



On Fri, Oct 26, 2018 at 2:30 PM David A Case <david.case.rutgers.edu> wrote:

> 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
>


-- 
*********************************************************
Dr. Jon Uranga
Institute of Physical Chemistry
Computational Chemistry and Biochemistry Group
Tammannstr. 6
37077 Göttingen
Germany
Office Phone: 33131
E-mail: jon.uranga.chemie.uni-goettingen.de
*********************************************************
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Received on Fri Oct 26 2018 - 06:00:06 PDT
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