Dear Amber users and developers,
I am trying to parameterize non-standard amino acids using mdgx and ff15ipq (AmberTools22).
I have encountered a problem quite early in the process.
I am working with norleucine. I created a mol2 file and edited the atom types of CA to CX, CB to 2C, CG to 3C and O to OD.
However, when I try to run parmchk using
parmchk2 -i NLE.mol2 -f mol2 -o NLE.frcmod -p /home/amin/softwares/amber22/dat/leap/parm/parm15ipq_10.3.dat
I get an error as follows
Atom type of OD does not exist in PARMCHK.DAT
If I replace OD with O, I get an frcmod file as expected.
The atom section of my input mol2 looks as follows after editing.
.<TRIPOS>ATOM
1 N -1.9680 0.0710 0.3120 N 1 NLE -0.251000
2 CA -1.2060 1.2220 -0.1620 CX 1 NLE -0.054000
3 C 0.2920 1.0090 0.0910 C 1 NLE 0.216000
4 O 0.7170 0.4370 1.0960 OD 1 NLE -0.217000
5 CB -1.7010 2.5050 0.5400 2C 1 NLE -0.190000
6 CG -1.3600 3.7940 -0.2280 3C 1 NLE -0.153000
7 CD -1.8050 5.0560 0.5250 CT 1 NLE -0.159000
8 CE -1.6020 6.3320 -0.2980 CT 1 NLE -0.211000
9 H -1.4810 -0.3330 1.1060 H 1 NLE 0.138000
10 HA -1.3700 1.3210 -1.2370 H1 1 NLE 0.142000
11 HB2 -2.7830 2.4620 0.6610 HC 1 NLE 0.095500
12 HB3 -1.2860 2.5590 1.5490 HC 1 NLE 0.095500
13 HG2 -1.8470 3.7630 -1.2030 HC 1 NLE 0.084500
14 HG3 -0.2880 3.8500 -0.4220 HC 1 NLE 0.084500
15 HD2 -2.8560 4.9750 0.8000 HC 1 NLE 0.079000
16 HD3 -1.2490 5.1380 1.4590 HC 1 NLE 0.079000
17 HE1 -1.8950 7.2150 0.2720 HC 1 NLE 0.074000
18 HE2 -0.5590 6.4580 -0.5890 HC 1 NLE 0.074000
19 HE3 -2.2040 6.3150 -1.2090 HC 1 NLE 0.074000
What am I doing wrong?
I would be really grateful for any suggestions.
Best,
Amin.
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Received on Tue Apr 25 2023 - 07:00:03 PDT
