On Feb 8, 2017, at 9:07 AM, Stellamaris Sotomayor Burneo <stellamaris_sb@yahoo.com> wrote:
Dear Dr. Eric,
My name is Stellamaris. I am an undergraduate student from Ecuador. There is almost no one working in molecular docking in my country so far. So, it is very difficult to find somebody to ask for help. I would like to kindly ask you a question about the problem I am having with Chimera and I would really appreciate your help.
I am trying to convert a set of receptors (named receptor.pdb) to receptor.mol2. using chimera. However i am having problems with the charges of FAD, NAD, NDP, and FMN. Receptors that have problems in those groups are not being transformed.
Is there a way to transform those files without having to change to charges? I have tried changing the charges and it seems to work. However, I am very afraid of changing the conditions of my simulations if I change the charges.
I have gotten the following message: NAD) Error: cannot run "/opt/UCSF/Chimera64-1.10.2/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit Failure running ANTECHAMBER for residue NAD
Hi Stellamaris, As you have discovered, the underlying tools that Chimera relies on to derive charges (AmberTools/antechamber/sqm) sometimes fail for entities with concentrated areas of negative charge. It is for this reason that Chimera already includes pre-calculated charges for ADP, ATP, GDP, and GTP. These charges were taken from the AMBER parameter database <http://research.bmh.manchester.ac.uk/bryce/amber>. Charges for the moieties you mentioned are also in that database, and I’ve gone ahead and added NAD and NDP to the ones that Chimera knows about without needing to do a calculation. Precalculated NAD/NDP charges will be available in daily builds dated Feb. 9 or later. Unfortunately, FMN and FAD are more problematic in that Chimera doesn’t protonate them in the standard way used in the database. It adds a proton (and positive charge) to the isoalloxazine ring system so that the central ring becomes aromatic. Obviously, the simplest way to deal with this if you don’t need FAD/FMN as a cofactor is to simply delete them. If you do need them then things get hairy. I guess what I would do is: 1) Delete FMN/FAD. 2) Run Dock Prep which will get you a Mol2 file of the remainder of the system with charges. 3) Close your system and reopen it. 4) Delete everything but the FMN/FAD. 5) Set the IDATM types of the FMN/FAD so that they correspond to the standard protonation pattern. 6) Add hydrogens. 7) Write another Mol2 file with just FMN/FAD. 8) Edit this second Mol2 file and transcribe the charges found in the corresponding Amber parameter database file to the atoms. 9) Combine your two Mol2 files. Step 6 is a little tricky in that the atom names in the “OFF” parameter files aren’t all the same as the PDB standard names, but there is connectivity information in the OFF file, so you can figure out which atom is which. You can do step 5 by running the “defattr” command with the file I have attached, which will set the types of FMN/FAD heavy atoms to the standard protonation pattern. Also, instead of step 8, you could work up another “defattr” file to assign charges to the FMN/FAD before you write out the Mol2 file. Probably easier. —Eric Eric Pettersen UCSF Computer Graphics Lab