David
Thank you very much for the reply.
I tried the flag -dr no. The resulting structure had wrong conectivities
and the overall charge was 0 and 1 carbon had 5 bonds.
Here is the structure:
11
-ISIS- 3D
14 15 0 0 0 0 0 0 0 0 0
-0.6220 2.1310 -3.7850 O 0 0 0 0 0
0.9470 -0.3750 -7.1350 O 0 0 0 0 0
1.5650 -1.1270 -5.0610 N 0 0 0 0 0
1.9600 -1.5360 -2.6640 N 0 0 0 0 0
0.2450 0.7630 -5.3960 N 0 0 0 0 0
1.6250 -0.9690 -1.4940 N 0 0 0 0 0
1.4460 -0.8650 -3.7370 C 0 0 0 0 0
0.7330 0.2060 -3.2120 C 0 0 0 0 0
0.0440 1.1440 -4.0900 C 0 0 0 0 0
0.8880 0.0750 -1.8240 C 0 0 0 0 0
0.9540 -0.3010 -5.9090 C 0 0 0 0 0
2.5310 -2.3670 -2.7210 H 0 0 0 0 0
-0.1950 1.3530 -6.0870 H 0 0 0 0 0
0.4700 0.7330 -1.0760 H 0 0 0 0 0
1 9 2 0 0 0
2 11 2 0 0 0
3 7 2 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 1 0 0 0
8 9 2 0 0 0
8 10 1 0 0 0
10 14 1 0 0 0
M END
George
> On Fri, Sep 18, 2020, Giorgos Lambrinidis wrote:
>>
>>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-)
>
> You can try setting '-dr no' to remove the valence check, and see what
> happens. But be sure to check the results carefully, since you will be
> outside the usual range of structures that GAFF has been built for.
> You should also add '-at gaff2' to get more up-to-date parameters.
>
> cc-ing to Junmei, in case he has comments here.
>
> ...dac
>
>
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>
--
“Good judgement is the result of experience and experience the result of
bad judgement.”
― Mark Twain
---------------------------------------------
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 - 08:30:03 PDT
