I have tested your molecule using your prepin and frcmod files. I also did
igb=1 minimization for 10,000 steps. I did not observe weird behavior of
amide groups. Please check if you can reproduce my result.
All the best
Junmei
On Fri, Apr 24, 2020 at 7:41 AM Arnaud Bondon <arnaud.bondon.univ-rennes1.fr>
wrote:
> Hello,
>
> below is a view of a structure after minimization (without NMR
> restraints). Clearly the N10 amide nitrogen
> has an pyramidal character. And the omega dihedral angles are not good
>
> The molecule was prepared as a mol2 file Nitrogen are N.am (see below)
> I tried to create the non natural amino acid
>
> Then
> antechamber -i testsirius4.mol2 -fi mol2 -o ./prep/testsirius4.prepin
> -fo prepi -c bcc -s 2 -nc 4 > ./prep/antechamber.out
>
> Something is wrong but where?
> Man thans by advance for any suggestion
>
> arnaud
>
>
> 92 N10 18.9273 -4.2156 -6.9272 N.am 1 UNK -0.3001
> 93 C28 19.2161 -4.9020 -5.6192 C.3 1 UNK 0.1305
> 94 C29 18.4539 -6.2190 -5.3899 C.2 1 UNK 0.2362
> 95 O7 17.3090 -6.3837 -5.7791 O.2 1 UNK -0.2737
> 96 C30 18.9294 -3.9948 -4.3811 C.3 1 UNK 0.1213
> 97 O8 17.5154 -3.7707 -4.2774 O.3 1 UNK -0.3842
> 98 C31 19.6691 -2.6414 -4.3199 C.3 1 UNK -0.0065
> 99 HN1 17.9521 -4.0328 -7.1379 H 1 UNK 0.1496
> 100 H28 20.2733 -5.1804 -5.6025 H 1 UNK 0.0623
> 101 H30 19.2454 -4.5518 -3.4937 H 1 UNK 0.0671
> 102 HO8 17.1331 -3.5231 -5.1721 H 1 UNK 0.2101
> 103 H311 20.7523 -2.7678 -4.2499 H 1 UNK 0.0839
> 104 H312 19.4179 -2.0212 -5.1828 H 1 UNK 0.0839
> 105 N11 19.1881 -1.9186 -3.0881 N.4 1 UNK 0.2204
> 106 HN11 19.4727 -2.3707 -2.1941 H 1 UNK 0.1995
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Received on Wed Apr 29 2020 - 08:00:02 PDT
