Running the AMBER FF on gromacs 4.0.5
I am using gromacs 4.0.5 with ffAmber test with gromacs 4. To set up the framework I followed the instructions outlined here:
http://www.somewhereville.com/?p=114
and here:
http://chemistry.csulb.edu/ffamber/
The first page details how to add the actual force field an let know gromacs how to select the different amber ffs. The second contains information about how pdb files should look like for gromacs/amber to understand them. For example, LYS should be renamed LYP when protonated. In the same fashion HIS are either HIP, HIE or HID. Now, the main reason I wanted to get amber to work with gromacs is the ability to use deprotonated CYS (called CYM) versus the normal CYS (CYN). Worthy of notice is that N- or C-termini residues should be indicated, for example, NASP or CASP. Of course, these are just a few examples. You should check the amber manual and/or the hdb files to make sure if you are picking the right residue.
A great advantage of the ffAMBER is that it can model Zn !!!
http://www.somewhereville.com/?p=114
and here:
http://chemistry.csulb.edu/ffamber/
The first page details how to add the actual force field an let know gromacs how to select the different amber ffs. The second contains information about how pdb files should look like for gromacs/amber to understand them. For example, LYS should be renamed LYP when protonated. In the same fashion HIS are either HIP, HIE or HID. Now, the main reason I wanted to get amber to work with gromacs is the ability to use deprotonated CYS (called CYM) versus the normal CYS (CYN). Worthy of notice is that N- or C-termini residues should be indicated, for example, NASP or CASP. Of course, these are just a few examples. You should check the amber manual and/or the hdb files to make sure if you are picking the right residue.
A great advantage of the ffAMBER is that it can model Zn !!!
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