Hello,
I was attempting to use the GFP simulation tutorial ( found atÂ
http://ambermd.org/tutorials/basic/tutorial5/index.htm) in order to create a non-standard residue for later use in a simulation of lipase. The modified amino acid that I was attempting to create (which I have called SMR) can be seen in the SMR_RESIDUE.pdb file (attached). However, after following the tutorial and doing everything it stated, I found tleap to be unable to correctly construct my residue- it was incorrectly bonding atoms that should not be bonded (more specifically, it was protonating a carbonyl oxygen that should not be protonated, amongst other issues). This is in spite of the atoms being in the correct position in three-dimensional space. I have attached the antechamber, prep, and frcmod files that I obtained and used in the process of completing the tutorial, as well as the leap command file and leap.log output from tleap. The input structure is the A_smr_A.pdb file, and the output that leap produced is the A_smr_A.wa.pdb file. Please let me know if there is a possible fix to this issue, and thank you in advance for your help.
Kind regards,
Siddharth Marwaha
Kind regards,
Siddharth Marwaha
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- application/octet-stream attachment: leap.log
- application/octet-stream attachment: LEAPY
- application/octet-stream attachment: smr.ac
Received on Mon Apr 27 2020 - 12:00:02 PDT
