[AMBER] Solvate a system in AMBER 11.

From: Sudarshan Debnath <suarshandebnath.ku.rediffmail.com>
Date: 31 Dec 2011 15:35:22 -0000

Dear Sir/Madam,

I am a user of AMBER 11. I want to simulate a nucleic acid system. I use TIP3P water model to solvate the system. This method adds water molecules at the surrounding region of the system, not in the cavities (or inner part or core part). Is there any procedure to solvate the cavities as well as surrounding region of the system? Please let me know.

By the way what I do as follows-

tleap –f leaprc.ff99SB

X=loadpdb nacid.pdb

addions X Na+ 0

solvateoct X TIP3PBOX 8.0

saveamberparm X nacid_solv.prmtop nacid_solv.inpcrd

savepdb X nacid_solv.pdb

According to many reference core part as well as surrounding part of a system can be solvated by immerge the system into a water box followed by remove the coordinates of overlaid water molecules. How to do this in AMBER 11?

With the Best Regards,


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Received on Sat Dec 31 2011 - 08:00:03 PST
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