Dear all
I want to prepare oxypurinol molecule using antechamber module, which
has a nitrogen charged (2 single bonds). When i run
antechamber -i 1.sdf -fi sdf -o 11.sdf -fo sdf -c bcc -nc -1
i get the error
/opt/AMBER/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (2) for atom (ID: 3, Name: N1).
Possible open valence.
the problems is found on the nitrogen which is charged (N-)
The input of my file is as follows:
--------------------
oxypurinol_charged
3D
Structure written by MMmdl.
14 15 0 0 1 0 999 V2000
-0.6223 2.1307 -3.7849 O 0 0 0 0 0 0
0.9471 -0.3746 -7.1353 O 0 0 0 0 0 0
1.5647 -1.1275 -5.0608 N 0 5 0 0 0 0
1.9602 -1.5361 -2.6636 N 0 0 0 0 0 0
0.2446 0.7632 -5.3964 N 0 0 0 0 0 0
1.6245 -0.9690 -1.4938 N 0 0 0 0 0 0
1.4465 -0.8651 -3.7372 C 0 0 0 0 0 0
0.7326 0.2059 -3.2116 C 0 0 0 0 0 0
0.0440 1.1438 -4.0900 C 0 0 0 0 0 0
0.8885 0.0753 -1.8242 C 0 0 0 0 0 0
0.9542 -0.3006 -5.9088 C 0 0 0 0 0 0
2.5306 -2.3670 -2.7215 H 0 0 0 0 0 0
-0.1951 1.3533 -6.0866 H 0 0 0 0 0 0
0.4704 0.7327 -1.0759 H 0 0 0 0 0 0
1 9 2 0 0 0
2 11 2 0 0 0
3 7 1 0 0 0
3 11 1 0 0 0
4 6 1 0 0 0
4 7 1 0 0 0
4 12 1 0 0 0
5 9 1 0 0 0
5 11 1 0 0 0
5 13 1 0 0 0
6 10 2 0 0 0
7 8 2 0 0 0
8 9 1 0 0 0
8 10 1 0 0 0
10 14 1 0 0 0
M CHG 1 3 -1
M END
--------------------
Any help would be appreciated.
Regards
George Lambrinidis
--
---------------------------------------------
Dr George Lambrinidis
Researcher & Laboratory Assistant Staff
School of Health Sciences
Faculty of Pharmacy
National & Kapodistrian University of Athens
Greece
tel: +30 2107274304
+30 2107274521
fax: +30 2107274747
e-mail: lambrinidis.pharm.uoa.gr
geolampr.gmail.com
---------------------------------------------
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Received on Fri Sep 18 2020 - 05:00:02 PDT
