AMBER Archive (2007)

Subject: Re: AMBER: Problem related simulation of dimer

From: Abhilash (mohan.25_at_osu.edu)
Date: Thu Mar 15 2007 - 10:03:06 CST

I had this same problem sometime back. Include blank spaces after the
'TER' card and also make a whole new line with empty spaces after the
'TER' card. I don't know how this works but it seemed to do the trick
for me. I think it is a minor bug in the code or something.
Best,
Abhilash Mohan
Carlos Simmerling wrote:
> seems like it should work, maybe if you look at the leap.log you'll
> see what it is doing.
>
> On 3/15/07, priya priya <priyaanand_27_at_yahoo.co.in> wrote:
>> Dear All
>> I am trying to run a simulation of dimer each chain has 16
>> residues.In the
>> pdb fileI added TER between the chains but when i use the command
>> edit in
>> xleap there is a bond between the chains. but i want two different
>> chains
>> and non bonded. I am attaching the pdb file with mail.
>> will anybody tell me the mistake.
>> Thanks in advance
>> Priya
>>
>>
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>>
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