Hi,
I used:
antechamber -i bi12.mol -fi mol -o bi12.mol2 -fo mol2
to generate bi12.mol2 using bi12.mol
but as you can see in the attached file, bi12.mol2 is almost empty with
no data.
Appreciate your help in advance!
Regards,
Sarvin
Wei Zhang wrote:
> Sure, just send it the list.
>
> Sincerely,
>
> Wei
>
> On Jan 28, 2009, at 2:21 PM, sarvin moghaddam wrote:
>
>> Hi Wei,
>>
>> Thanks a lot for your help. I used:
>> antechamber -i test.mol -fi mol -o test.mol2 -fo mol2
>>
>> and unfortunately my mol2 files is almost empty. Is that OK if I send
>> you my "mol" file and you take a look at your convenient time. I
>> appreciate you help in advance!
>>
>> Thanks a lot!
>> Sarvin
>>
>>
>>
>> Wei Zhang wrote:
>>> Hi,
>>>
>>> No, you cannot do that. You must go through leap (tleap or sleap).
>>>
>>> 1. you can use antechamber to generate a mol2 file
>>>
>>> antechamber -i test.mol -fi mol -o test.mol2 -fo mol2
>>>
>>> the generated mol2 file will have charge amber and atom type
>>>
>>> 2. use leap to load the generated mol2 file, and generate top file
>>> you need write a script like the following:
>>>
>>> source leaprc.gaff
>>> m = loadmol2 test.mol2
>>> saveamberparm m test.top test.xyz
>>>
>>> save it as test.lrc, then
>>>
>>> sleap < test.lrc
>>>
>>> Sincerely,
>>>
>>> Wei
>>>
>>>
>>> On Jan 28, 2009, at 1:49 PM, sarvin moghaddam wrote:
>>>
>>>> Hi,
>>>>
>>>> I was wondering if I can generate the top file using antechamber
>>>> having the mol file. I know it should sound very trivial for Amber
>>>> users but I am a beginner and have read all the antechmaber related
>>>> parts in Amber manual and also the paper by Case et. al. But still
>>>> was wondering if I only can get the top file by:
>>>>
>>>> antechamber -i test.mol -fi mol -o test.? -fo ?
>>>>
>>>> I have the mol file generated by ACD/ChemSketch
>>>>
>>>> Appreciate your help.
>>>>
>>>> Thanks!
>>>> Sarvin
>>>>
>>>>
>>>>
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>>>
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>
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ACD/Labs10150708433D
34 35 0 0 0 0 0 0 0 0 2 V2000
15.2806 -11.7203 -1.4423 C 0 0 0 0 0 0 0 0 0 0 0 0
16.1859 -12.5871 -0.5344 C 0 0 0 0 0 0 0 0 0 0 0 0
16.1412 -10.9078 -2.4318 C 0 0 0 0 0 0 0 0 0 0 0 0
17.6685 -12.3682 -0.8982 C 0 0 0 0 0 0 0 0 0 0 0 0
16.9675 -11.8914 -3.2856 C 0 0 0 0 0 0 0 0 0 0 0 0
17.8744 -12.7560 -2.3770 C 0 0 0 0 0 0 0 0 0 0 0 0
17.1060 -10.0092 -1.6322 C 0 0 0 0 0 0 0 0 0 0 0 0
18.0092 -10.8747 -0.7214 C 0 0 0 0 0 0 0 0 0 0 0 0
15.2475 -10.0538 -3.3328 C 0 0 0 0 0 0 0 0 0 0 0 0
18.5620 -13.2252 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.4856 -9.1050 -2.5086 N 0 3 0 0 0 0 0 0 0 0 0 0
18.2136 -14.6427 -0.1714 N 0 3 0 0 0 0 0 0 0 0 0 0
14.5918 -12.3796 -2.0126 H 0 0 0 0 0 0 0 0 0 0 0 0
14.6889 -11.0216 -0.8130 H 0 0 0 0 0 0 0 0 0 0 0 0
16.0239 -12.3021 0.5272 H 0 0 0 0 0 0 0 0 0 0 0 0
15.9294 -13.6590 -0.6739 H 0 0 0 0 0 0 0 0 0 0 0 0
16.2775 -12.5520 -3.8528 H 0 0 0 0 0 0 0 0 0 0 0 0
17.5990 -11.3169 -3.9966 H 0 0 0 0 0 0 0 0 0 0 0 0
18.9377 -12.5912 -2.6539 H 0 0 0 0 0 0 0 0 0 0 0 0
17.6176 -13.8283 -2.5134 H 0 0 0 0 0 0 0 0 0 0 0 0
17.7401 -9.4330 -2.3395 H 0 0 0 0 0 0 0 0 0 0 0 0
16.5165 -9.3062 -1.0056 H 0 0 0 0 0 0 0 0 0 0 0 0
17.8474 -10.5858 0.3391 H 0 0 0 0 0 0 0 0 0 0 0 0
19.0736 -10.7079 -0.9930 H 0 0 0 0 0 0 0 0 0 0 0 0
15.8659 -9.4798 -4.0556 H 0 0 0 0 0 0 0 0 0 0 0 0
14.5316 -10.6980 -3.8868 H 0 0 0 0 0 0 0 0 0 0 0 0
19.6297 -13.0862 -0.2741 H 0 0 0 0 0 0 0 0 0 0 0 0
18.4139 -12.9493 1.0659 H 0 0 0 0 0 0 0 0 0 0 0 0
15.5227 -8.2723 -2.5086 H 0 0 0 0 0 0 0 0 0 0 0 0
13.6529 -8.0680 -2.5086 H 0 0 0 0 0 0 0 0 0 0 0 0
13.4486 -9.9378 -2.5086 H 0 0 0 0 0 0 0 0 0 0 0 0
16.9220 -14.3252 -0.1714 H 0 0 0 0 0 0 0 0 0 0 0 0
17.8960 -15.9342 -0.1714 H 0 0 0 0 0 0 0 0 0 0 0 0
19.5051 -14.9602 -0.1714 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
2 4 1 0 0 0 0
3 5 1 0 0 0 0
4 6 1 0 0 0 0
6 5 1 0 0 0 0
3 7 1 0 0 0 0
4 8 1 0 0 0 0
8 7 1 0 0 0 0
3 9 1 0 0 0 0
4 10 1 0 0 0 0
9 11 1 0 0 0 0
10 12 1 0 0 0 0
13 1 1 0 0 0 0
14 1 1 0 0 0 0
15 2 1 0 0 0 0
16 2 1 0 0 0 0
17 5 1 0 0 0 0
18 5 1 0 0 0 0
19 6 1 0 0 0 0
20 6 1 0 0 0 0
21 7 1 0 0 0 0
22 7 1 0 0 0 0
23 8 1 0 0 0 0
24 8 1 0 0 0 0
25 9 1 0 0 0 0
26 9 1 0 0 0 0
27 10 1 0 0 0 0
28 10 1 0 0 0 0
29 11 1 0 0 0 0
30 11 1 0 0 0 0
31 11 1 0 0 0 0
32 12 1 0 0 0 0
33 12 1 0 0 0 0
34 12 1 0 0 0 0
M CHG 2 11 1 12 1
M END
.<TRIPOS>MOLECULE
MOL
0 0 1 0 0
SMALL
No Charge or Current Charge
.<TRIPOS>ATOM
.<TRIPOS>BOND
.<TRIPOS>SUBSTRUCTURE
1 MOL 1 TEMP 0 **** **** 0 ROOT
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Received on Fri Jan 30 2009 - 01:30:39 PST
