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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
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>
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Received on Fri Jan 30 2009 - 01:30:27 PST
