Re: [AMBER] Antechamber

From: Jasim, Mahmood (Student) <"Jasim,>
Date: Tue, 17 Sep 2013 12:09:21 +0000

Dear Sir The files that I used are attached to the messege, complex.pdb is the conformation of the protein-ligand complex that I started the calculation with, LIG.pdb is the conformation of the ligand alone, LIG.prepin and LIG.frcmod are the files generated by Antechamber for the ligand and vac.inpcrd is the inpcrd file generated for the ligand. I could not load any more files because of the upload limit of the mailing list. The commands that I used are: nohup $AMBERHOME/exe/antechamber -i LIG.pdb -fi pdb -o LIG.prepin -fo prepi -c bcc -s 2 & $AMBERHOME/exe/parmchk -i LIG.prepin -f prepi -o LIG.frcmod $AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB source leaprc.gaff loadamberprep LIG.prepin loadamberparams LIG.frcmod model=loadpdb complex.pdb addions model Na+ 0 saveamberparm model vac.prmtop vac.inpcrd My ligand is not charged and I am using AMBER 12 on a GPU. When I convert the inpcrd file to pdb file using this command: $AMBERHOME/exe/ambpdb -p vac.prmtop < vac.inpcrd > vac_inpcrd.pdb the ligand position within the protein in the resulting file is different from the starting conformation in complex.pdb and the ligand itself is distorted. I am using different ligands on the same protein and I am getting this with all of them. Thank you so much for your patience Mahmood Jasim ________________________________________ From: David A Case [] Sent: 17 September 2013 12:36 To: AMBER Mailing List Subject: Re: [AMBER] Antechamber On Tue, Sep 17, 2013, Jasim, Mahmood (Student) wrote: > > I have tried your suggestion and not solvate the system. The results > were similar. I have attached the files for you to have a look please. Unfortunately, what you sent is not enough to even understand the problem, let alone to reproduce it. As I remember(?), you didn't have any LIG.pdb file in your earlier post. If you are going to get help, you will need to post (again) the exact commands you used, provide all the needed files, and describe the problem in as much detail and specificity as you can. (That is, don't just say, the "the pdb file I get from ambpdb is bad"; give an example of exactly what you don't like about the result.) What you seem to be doing is what we do every day with this code, so no one is likely to say: "Oh, I recognize that problem". We have to be able to try to reproduce the problem. You can help by trying to find a simple and small example that illustrates it. Does this happen with every protein-ligand complex you try, or just this particular one? ...dac _______________________________________________ AMBER mailing list

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Received on Tue Sep 17 2013 - 05:30:07 PDT
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