AMBER Archive (2008)

Subject: Re: AMBER: ptraj center problem

From: robaldo_at_dna.uba.ar
Date: Fri Nov 21 2008 - 14:04:56 CST

Thank you Carlos it works!!

yes, I have 24 resids

On Fri, November 21, 2008 3:42 pm, Carlos Simmerling wrote:
> not sure why it isn't working- I use this and have no trouble
>
> center :1-198 mass origin image origin center familiar
>
>
> do you have only one molecule in :1-24? have you applied all patches?
>
>
>
>
> On Fri, Nov 21, 2008 at 12:31 PM, <robaldo_at_dna.uba.ar> wrote:
>
>> Dear amber users,
>>
>>
>> I'm working in modified nucleic acid molecular dynamics. I use tleap to
>> add ions and make an octahedral box water. Then, when I finish the
>> dynamic and I try to make a center and complete trajectory file using
>> the individual trajectories, ptraj doesn't center the water and the
>> octahedral box lost shape. While I always use the same protocol and the
>> same ptraj.in to do that, it only happens sometimes. Therefore, when I
>> try to calculate the hydratation I have lots of errors.
>>
>>
>> I'm using the following ptraj.in:
>>
>>
>> #******* ptraj center
>>
>>
>> rm -f ptraj.in
>>
>> cat <<eof > ptraj.in
>>
>> trajin ../x_3ns.tra trajin ../x_4ns.tra trajin ../x_5ns.tra trajin
>> ../x_6ns.tra
>> trajin ../x_7ns.tra trajin ../x_8ns.tra trajin ../x_9ns.tra trajin
>> ../x_10ns.tra
>>
>>
>> center :1-24 image center byres familiar trajout x.tra
>>
>> eof
>>
>> ptraj ./x.top < ptraj.in > ptraj.out
>>
>>
>> thanks,
>>
>> best regards,
>>
>> Laura
>>
>>
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