Also make sure that you are using ambertools 16
(Double check your AMBERHOME env)
Hai
> On Mar 21, 2017, at 7:00 PM, Jon Mujika <joni.mujika.ehu.es> wrote:
>
> Dear Amber users,
>
>
> I want to simulate a polymer in solution. Since this is the first time I am
> trying to do something like this, I followed Tutorial A27, where a similar
> polymer is prepared in the gas-phase. I managed to set up the system in the
> gas-phase, but the problem comes when I try to solvate the system. To do
> that, I modified a tleap input that I used previously with success to set
> up a protein system:
>
>
> source leaprc.gaff
>
> source leaprc.water.tip3p
>
> loadamberprep peg.prepi
>
> loadamberprep hpg.prepi
>
> loadamberprep tpg.prepi
>
> mol = sequence {HPG PEG PEG PEG PEG PEG PEG PEG PEG PEG PEG PEG PEG PEG PEG
> PEG PEG PEG PEG TPG}
>
> solvateoct mol TIP3PBOX 12.0
>
> saveAmberParm mol peg.prmtop peg.inpcrd
>
> savepdb mol peg.pdb
>
> quit
>
>
> But to my surprise, the topology file is not generated, and looking at the
> leap.log file, I found the following:
>
>
>> source leaprc.water.tip3p
>
> Could not open file leaprc.water.tip3p: not found
>
>
> But as I said, I used the input file for another system, and tleap found
> the “leaprc.water.tip3p” file and solvated the system without any error.
> The only remarkable difference is that I loaded the “leaprc.protein.ff14SB”
> instead of “leaprc.gaff”. Can anyone please provide an explanation for this
> issue?
>
>
> Many thanks in advance,
>
>
> Jon Mujika
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Received on Wed Mar 22 2017 - 09:30:02 PDT
