Hii,
I sent a mail regarding this problem before and attached two
files. But due to larger size of files that is not posted. So, I am
writing once more. I am going to do a simulation of human carbonic
anhydrase II using 2CBA.pdb. As it lacks of two N-terminal
residues(NMET and SER) I attached them with the help of SWISS PDB
VIEWER. Here some unwanted bond is formed between NMET and crystal
waters. I thought after minimization those bonds will be removed and I
would get a good structure. But in pmemd.cuda those bonds are not
removing. Then I tried it in sander. Here those bonds are removing
very soon. Then I ran pmemd.cuda for second minimization with no
constraint. It ran well. Now when I am trying to heat the system from
0K to 300K by pmemd.cuda I am getting a error message. It is-
" Hydrogen atom 4102 appears to have multiple bonds to atoms 4103 and
4102 which is illegal for SHAKEH.
Exiting due to the presence of inconsistent SHAKEH hydrogen clusters."
Atoms 4102 and 4103 are H atoms of water molecule which is bonded to
zinc ion at active site. Here also when I heat the system in sander no
problem comes. It is bothering me too much. I checked the distance
between the atoms 4102 and 4103. It is alright. When I prepared the
system I used a '.off' file for the water bonded to Zn ion as the
charges of atoms of this water molecule would be different from other
water molecules. I am attaching this file here. Please help me. If
anyone has any other query please let me know.
Thanking you.
Sanjib Paul
Indian Institute of Technology, Kharagpur,
India.
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- application/octet-stream attachment: wat.off
Received on Tue Jan 29 2013 - 04:30:03 PST
