AMBER Archive (2009)

Subject: Re: [AMBER] ambmol2?

From: Junmei Wang (junmwang_at_gmail.com)
Date: Tue Mar 31 2009 - 21:41:35 CDT

Hi,
I will improve the code so that it can handle atom names of five characters.

Best

Junmei

On Tue, Mar 31, 2009 at 9:15 PM, Taufik Al-Sarraj <
taufik.alsarraj_at_utoronto.ca> wrote:

> 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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>
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