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 Tue Mar 21 2017 - 16:30:02 PDT
