Dear Amber users,
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.
Obviously, I can see that the CX is not present in PARMCHK.dat. Therefore,
I have done the test of substituting CX by CT and in this case parmchk2
works for both amber versions. Then, I was thinking to manually substitute
the bonded, angle, dihedral and impropers, using parmed.py, since the
charges are taken from prepi file and the lennard jones parameters are the
same for CX and CT. I would set them up to the usual values of a LYS due to
the fact that CX is the C_alpha. Or maybe a simpler option would be to
directly substitute them by the adequate values in the obtained frcmod
file, based on the parm10.dat file.
However, there is one more thing that I am confused with: the obtained
frcmod file complains about some parameters which I do not think it should
be present or should be modified:
CT-O 0.00 0.000 ATTN, need revision
In this particular case, I do not have any bond involving CT-O, indeed,
both oxygen atoms are connected to C atom types, as they are carbonyls, as
indicated in parm10.dat (I am using ff14SB). Therefore, I can safely erase
it.
The overall parameters that need revision involve also the following ones:
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
Again, I think some of the parameters should not be present as they are:
-C -O -CT, the correct order should have been CX-C -O and CT-C -O
Correct value from parm10.dat file:
CT-C -O 80.0 120.40
CX-C -O 80.0 120.40 (was CT-C-O)
-HC-CT-O is not applicable in this case, instead, it should be HC-CT-C
Correct value from parm10.dat file:
C -CT-HC 50.0 109.50 AA gln changed based on NMA nmodes
-C -CT-O should be the same as the first one (O -C -CT or CT-C -O)
Correct value from parm10.dat file:
CT-C -O 80.0 120.40
-HC-CT-O -C should be HC-CT-C -O and H1-CX-CT-O
Correct value from parm10.dat file:
X -CT-CT-X 9 1.40 0.0 3.
JCC,7,(1986),230
X -CT-CX-X 9 1.40 0.0 3.
JCC,7,(1986),230 (was X -CT-CT-X )
-C -CT-O -C there are not any C atom types to interact in such a way. So,
I think I can safely erase it.
All in all, I can manually substitute the erroneous values in the frcmod
file, but I would appreciate it if you could tell me the reason to get
those values in this file and most importantly for myself, would the
proposed corrections lead to an adequate frcmod file? Or am I making an
error in the procedure which makes parmchk2 to bring those values to the
frcmod file?
This is my ack.prepin file:
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 H13 H1 E 6 4 3 1.109 107.030 95.404 -0.006915
8 C6 CT M 6 4 3 1.547 111.272 -146.729 -0.039565
9 H11 HC E 8 6 4 1.102 107.503 -177.588 0.016237
10 H12 HC E 8 6 4 1.104 108.745 68.966 0.016237
11 C5 CT M 8 6 4 1.516 113.400 -54.995 -0.018750
12 H9 HC E 11 8 6 1.102 111.062 70.284 0.025229
13 H10 HC E 11 8 6 1.105 109.485 -46.564 0.025229
14 C4 CT M 11 8 6 1.551 110.064 -166.019 -0.032437
15 H7 HC E 14 11 8 1.101 109.676 49.548 0.060798
16 H8 HC E 14 11 8 1.103 110.699 -69.045 0.060798
17 C3 CT M 14 11 8 1.528 111.039 168.069 -0.161996
18 H5 HP E 17 14 11 1.102 111.828 61.840 0.144740
19 H6 HP E 17 14 11 1.101 109.619 -58.340 0.144740
20 N1 N M 17 14 11 1.458 110.078 -177.270 -0.623260
21 H4 H E 20 17 14 1.013 117.634 -99.492 0.391979
22 C2 C M 20 17 14 1.335 124.072 79.476 0.856166
23 O1 O M 22 20 17 1.239 123.377 -1.037 -0.585333
24 C1 CT M 23 22 20 2.372 33.778 -178.387 -0.390005
25 H1 HC E 24 23 22 1.101 142.117 -6.441 0.117754
26 H2 HC E 24 23 22 1.101 94.396 122.546 0.117754
27 H3 HC E 24 23 22 1.100 91.041 -130.354 0.117754
28 C8 C M 24 23 22 9.191 37.007 48.191 0.319291
29 O2 O E 28 24 23 1.240 78.604 120.320 -0.450617
LOOP
IMPROPER
C2 C3 N1 H4
C1 N1 C2 O1
C7 +M C8 O2
DONE
STOP
Many thanks for your help!
Best regards,
Jon Uranga
--
*********************************************************
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 - 04:00:03 PDT
