I don't see atom type OD used anywhere other than the ipq force fields.
it looks to me that ff15ipq might not be supported in parmchk2, but you
might want to contact the ff15ipq authors to find out.
I am not sure if they read messages on this email list.
On Tue, Apr 25, 2023 at 9:28 AM aamin.sagar--- via AMBER <amber.ambermd.org>
wrote:
> 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 - 07:00:02 PDT
