AMBER Archive (2009)

Subject: Re: [AMBER] ambmol2?

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Tue Mar 31 2009 - 21:15:00 CDT

Hi Junmei,
Thank you, the command works, but unfortuantely it turned out that atoms
with more than 4 digits are converted in the *.prmtop file into 4 digits
only. So the new mol2 file is not correct as Si400 is written as i400
and H1400 is written as 1400.

I have to modify my initial mol2 file in order to make this work.

Junmei Wang wrote:
> try top2mol2.
>
> Best
>
> Junmei
>
> On Tue, Mar 31, 2009 at 5:28 PM, Taufik Al-Sarraj <
> taufik.alsarraj_at_utoronto.ca> wrote:
>
>> Hi,
>>
>> Is the an ambmol2 function in amber? i would like to use
>> ambpdb -p *.prmtop < *.rst> *.pdb
>>
>> but to create a mol2, unfortunately i cannot create a pdb file because i
>> have some atoms named Si400 or H1400 which exceeds the number of digits
>> allowed in pdb.
>>
>> alternatively, is there a way to load *.prmtop and *.rst files in x/t/sleap
>> and use the savemol2 function?
>>
>> Best,
>> Taufik
>>
>>
>>
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