[gmx-users] Converting Amber frcmod and mol2 files to Gromacs
Simon Dürr
simon.duerr at uni-konstanz.de
Wed Sep 30 21:25:57 CEST 2015
Hi Michael,
thanks for the comment. I did not know the program.
It is however not what I'm looking for.
If you have a PDB that makes use of a residue not defined in your
desired FF (in my case Amber99SB-ILDN) and want to use pdb2gmx you
have no other choice than adding it to the FF by hand.
As I did not find good information about it I made this tutorial.
Cheers,
Simon
2015-09-30 13:54 GMT-04:00 Michael Shirts <mrshirts at gmail.com>:
> 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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