[gmx-users] Converting Amber frcmod and mol2 files to Gromacs
Michael Shirts
mrshirts at gmail.com
Wed Sep 30 19:54:31 CEST 2015
ParmEd (http://parmed.github.io/ParmEd/html/index.html) is an
interesting new tool that can help automate such conversions so they
don't need to be done as manually in the future.
On Wed, Sep 30, 2015 at 1:37 PM, Simon Dürr <simon.duerr at uni-konstanz.de> wrote:
> Hi,
>
> we had the pleasure to convert the *.mol2 and *.frcmod for the HEME
> and CYP prosthetic groups from the following paper for use with
> GROMACS:
> Shahrokh, K., Orendt, A., Yost, G. S. and Cheatham, T. E. (2012),
> Quantum mechanically derived AMBER-compatible heme parameters for
> various states of the cytochrome P450 catalytic cycle. J. Comput.
> Chem., 33: 119–133. doi: 10.1002/jcc.21922
>
> As the protocol for doing so is rather lengthy we want to share our
> protocol with you guys.
> If you can spare some time we would be grateful If some of you could
> check our procedure.
> If you find any errors let us know. However so far the trajectories
> look good (angles and bond distances are good).
>
> After further testing of the trajectories we want to release the
> rtp/hdb/itp - files.
> Where would be the best way to upload them?
>
> The Protocol is as follows:
>
>
> #################################
> ## Table of Contents ##
> #################################
> Part 1: RTP-file
> Part 2: ffbondend-file
> Part 3: ffnonbonded
> Part 4: residuetypes.dat
> Part 5: specbond.dat
> Part 6: hdb-file
> Part 7: atomtypes.atp
>
> ##########################
> ## PART 1 ##
> ##########################
>
> ##### BEGIN RTP-File #######
>
> [ HEME ]
> [ atoms]
> NC ncr 0.00660 1
> C1C ccr -0.01920 2
> C4C ccr -0.01930 3
> C2C ccr 0.01140 4
> C3C ccr -0.03570 5
> …
> [ bonds ]
> NC C1C
> NC C4C
> NC FE
> […]
> ###### END RTP-FILE #####
>
> The information to fill this file is found in the HEM.mol2 file.
>
> ###### HEM.mol2 ######
> @<TRIPOS>ATOM
> 1 NC 2.946000 -0.972000 -0.732000 nc 1 HEM 0.0066 ****
> 2 C1C 4.282000 -0.756000 -0.518000 cc 1 HEM -0.0192 ****
> 4 C2C 5.025000 -1.989000 -0.700000 cc 1 HEM 0.0114 ****
> 5 C3C 4.097000 -2.957000 -1.046000 cc 1 HEM -0.0357 ****
> […]
> @<TRIPOS>BOND
> 1 1 2 1
> 2 1 3 1
> 3 1 28 1
> ###### END HEM.mol2 #####
>
> To convert to Gromacs
> 1. take the uppercase name in column 2 of the mol2 which is the name
> found in the PDB input file and put it in column 1 of the [atoms]
> section of the .rtp
> 2. Add the lowercase identifier for GAFF (column 6 in the mol2 ) to
> the second column of the atoms section.
> 3. As we don't want to overwrite any of the normal definitions from
> AMBER99SB-ILDN with GAFF definitions we use a unique name for the GAFF
> atoms. Here we just added "r" at the end of each atom name.
> 4. Add the column 6 of the mol2 with the charge as third column to the
> atoms section
> 5 Group the atoms to charge groups in the fourth column of the
> [atoms]-section. We put every atom in a new group.
>
> Look at the bonds section in the mol2:
> The first column is the index of the bond, the second column is the id
> of the first atom of the bond, the third column the id of the second
> atom of the bond. The last is the bond type (single or double bond)
>
> 7.Take the id of the first atom and replace it with the uppercase
> identifier from the ATOM section of the mol2. Do the same for the id
> of the second atom.
>
> The columns 1,3,4,5,7 and 8 in the ATOM section are not relevant for Gromacs.
>
>
> ##########################
> ## PART 2 ##
> ##########################
>
>
> ##### BEGIN FFBONDED.ITP #####
> [ bondtypes ]
> ; i j func b0 kb
> fer ncr 1 0.2 83680 ; IC6.frcmod
> [..]
> [ angletypes ]
> ; i j k func th0 cth
> ncr fer ndr 1 85.521 1104.576 ; IC6.frcmod
> [..]
> [ dihedraltypes ]
> ;i j k l func phase kd pn
> X SH fer X 9 180.0 37.65600 2 ; IC6.frcmod
> [..]
> [ dihedraltypes ]
> X orr crr orr 4 180.0 4.60240 2 ; GAFF.dat improper
>
> #### END FFBONDED.ITP #####
>
> The information for this file can be found in the IC6.frcmod file OR
> in the gaff.dat
>
> #### IC6.frcmod #####
> BOND
> fe-nc 100.000 2.000
> [..]
> ANGLE
> nc-fe-nd 132.000 85.521 # average angle
> [..]
> DIHEDRAL
> X -SH-fe-X 1 9.000 180.000 2.000
> [..]
> IMPROPER
>
> NONBON
> fe 1.8 0.01 1.0
> #### END IC6.frcmod ####
>
> #### BEGIN GAFF.dat ###
> […]
> X -c -c -X 4 1.200 180.000 2.000
> X -o -c -o 1.1 180. 2. JCC,7,(1986),230
> #### END GAFF.dat #####
>
> To convert to Gromacs
> 1. Add the bonds section:
> a) Copy the two names of the atoms of the bond. Rename to new
> identifier and separate by a single space.
> b) Set func to 1 (single bond)
> c) Convert the b0 value from the Amber b0 value(in angstroms) as follows
>
> b0(Gro) = b0(amber) / 10 = [nm]
>
> d) Convert the kb value from the Amber kb value as follows:
>
> kb(Gro) = kb(amber) /10 *2 *4.184 = [joule]
>
> 2. Add the Angle section
> a) Copy the three names of the atoms of the angle. Rename to new
> identifier and separate by a single space.
> b) Set func to 1 (single bond)
> c) Copy the angle from amber
> d) Calculate cth as follows
>
> E(amber) = Emin/2
> cth = E(amber) *2 * 4.184 = [joule]
>
> 3. Add the dihedrals.
> First add all the dihedrals specified in the frcmod. Then use
> Ambertools to generate a coordinate and topology file with the loaded
> mol2 and frcmod files but don't load the GAFF parameters. Ambertools
> will tell you which impropers and dihedrals you have to add from the
> GAFF.dat because it could not find them in the frcmod.
>
> For each dihedral/improper do this:
> a) Copy the 4 names of the atoms of the dihedral. Rename the GAFF
> residues to your new identifier. Don't rename X and residues in
> uppercase
> b) Set func to 9 for a dihedral, set func to 4 for improper
> c) Take the phase from the fourth column of the Amber file
> d) Calculate the kd value:
> For dihedral (IDIVF is the second column in the Amber file)
>
> kd(gro) = PK(amber) * 4.184 / IDIVF(amber) = [joule]
>
> For impropers (IDIVF is not set)
>
> kd(gro) = PK(amber) *4.184 = [joule]
>
> d) Copy the pn value from the fifth column of the Amber file
>
> ##########################
> ## PART 3 ##
> ##########################
>
> #### BEGINf ffnonbonded.ITP ####
>
> [ atomtypes ]
> ; name at.num mass charge ptype sigma epsilon
> ncr 7 14.01 0.0000 A 3.25000E-01 7.11280E-01 ; GAFF.dat
> ccr 6 12.01 0.0000 A 3.39967E-01 3.59824E-01 ; GAFF.dat
> [...]
> #### END ffnonbonded.ITP ####
>
> #### BEGIN Mol.2 ####
>
> @<TRIPOS>ATOM
> 1 NC 2.946000 -0.972000 -0.732000 nc 1 HEM 0.0066 ****
> 2 C1C 4.282000 -0.756000 -0.518000 cc 1 HEM -0.0192 ****
>
> #### END Mol2 ####
>
> #### BEGIN GAFF.dat ####
>
> MOD4 RE
> cc 1.9080 0.0860 OPLS
>
> #### END GAFF.dat
>
>
> To convert to Gromacs:
> a) Copy the lowercase name of the atom in column six from the mol2 and
> rename to your new unique identifier.
> b) Set atomic number from the periodic table. Easy ;)
> c) Set mass from the periodic table or just copy it from other
> definitions in this file from the same element
> d) Set Charge to 0.000 which is the default value in Amber in Gromacs
> in this file.
> e) Set ptype to A
> f) Calculate sigma from the Rmin/2 value (second column in Gaff.dat
> MOD4 section)
>
> sigma = Rmin(amber) * 1/(2^(1/6)) *2 * 1/10
>
> g) Calculate Epsilon from the Epsilon value of Amber (third column in
> Gaff.dat MOD4 section)
>
> epsilon = epsilon(amber) *4.184 = [joule]
>
> ##########################
> ## PART 4 ##
> ##########################
>
> #### BEGIN Residuetypes.dat ####
>
> GLY Protein
> HEME Protein
> [..]
> #### END residuetypes.dat ####
>
> Add your new resname with the PDB Name here and assign it to the right group.
>
> ##########################
> ## PART 5 ##
> ##########################
>
> #### BEGIN specbond.dat ####
> [..]
> resA atomA nbondsA resB atomB nbondsB length newresA newresB
> CYS SG 1 HEM FE 2 0.2 CYP
> HEME
> [..]
> #### END specbond.dat
>
> Rename special residues like the CYS connected to the heme iron.
> Gromacs detects what it has to rename by the bond length which is the
> parameter in column 7 (in nanometers).
> For each of your residues you need a line here.
>
> ##########################
> ## PART 6 ##
> ##########################
>
> #### BEGIN HDB-File ####
>
> HEME 16
> ;nH type Name C-Atom Controlatoms
> 1 1 HHD CHD C1D C4C
> 1 1 HAC CAC C3C CBC
> 2 3 HBC CBC CAC C3C
> 3 4 HMC CMC C2C C1C
> [...]
> #### END HDB FIle #####
>
> There is no equivalent for this file in Amber. Just open the PDB file
> for your residue in a viewer(like UCSF Chimera) and let it display
> the atom names. What you now have to do is to add each hydrogen bond
> to its C atom and specify two control atoms.
>
> The index after the residue name(HEME 16) is the number of times a new
> hydrogen is defined.
> For each C atom you now have to add the hydrogens.
> Type can either be:
> 1: Planar hydrogens
> 2: single hydrogen
> 3: two planar hydrogens -CR=CH2
> 4: two or three tetrahedral hydrogens
> Others see: Gromacs Manual , chapter 5.6.4
>
> ##########################
> ## PART 7 ##
> ##########################
>
> #### BEGIN ATOMTYPES.ATP ####
> ncr 14.01000 ; GAFF.dat Sp2 N in non-pure aromatic systems
> ccr 12.01000 ; GAFF.dat Sp2 carbons in non-pure aromatic systems
> cgr 12.01000 ; GAFF.dat Inner Sp carbons in conjugated systems
>
> Add the same mass for the new atomtypes from the ffbonded.itp
> #### END atomtypes.atp ####
>
> ##########################
> ## Finalization ##
> ##########################
>
> After having done all this make a new folder in the Gromacs share
> folder to add your new FF as a duplicate of the old one with the new
> additions added.
>
> Closely examine the Gromacs log for errors or warnings.
> --
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