For example OH of carboxyl group and Phenolic OH group has same atoms and bond length but slightly different charges.
But how the gromacs will differentiate from the datas it gets from Pdb file?
Assuming pdb file contains only coordinates of different atoms.
PDB files don't contain only coordinates - they contain atom and residue names. Every GROMACS force field has files (extension .rtp - residue topology) that instruct pdb2gmx on how to build the topology of each given residue. The atom names differentiate elements of the same type.
Thank you very much sir for your reply.
In my procedure regarding Graphene Oxide
In GROMACS
Editconfig Pdb to gro
x2top to get the topology file : Opsala force field. ( I edited and made a folder in my working directory Opsala.ff)
Sorry If I am wrong. Gromacs guess the bond type referencing from .n2t and .itp file (Standard Bond distance given in those files) it measures actual distance from PDB/GRO file and designates the type (Like CN CE bellow) in topology file TOP file.
Sorry but I still could not find a way how gromacs differentiate same atom pairs and bond length having different charges from info in Pdb files
I created my molecule in VMD then used Avogadro to edit the molecules saved as pdb.
Few lines of .pdb file
HETATM 1 C 2 -0.850 1.180 -0.429 C
HETATM 2 C 2 2.680 3.017 -0.055 C
HETATM 3 C 2 5.032 0.335 -0.501 C
Few lines for .gro file
GRoups of Organic Molecules in ACtion for Science
263
2 C 1 0.486 0.622 1.456
2 C 2 0.839 0.806 1.493
atomname2type.n2t
Contains bond distancs
Few lines of .n2t file
C CN 0.00 12.011 4 H 0.108 C 0.140 C 0.140 C 0.140
C CE 0.14 12.011 4 C 0.1529 C 0.151 C 0.151 O 0.141 ;Epoxy
Few lines Force field.itp
[ atomtypes]
CN 6 12.01100 0.000 A 3.55000e-01 2.92880e-01
HB 1 1.00800 0.06 A 2.42000e-01 1.25520e-01
[ bondtypes ]
CN CN 1 0.14000 392459.2
CN CE 1 0.14000 392459.2
[ angletypes ]
CN CN CN 1 120.000 527.184
CN CN CE 1 120.000 527.184
CE CE CE 1 120.000 527.184
[ dihedraltypes ]
CN CN CN CN 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000
CE CN CN CE 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000
x2top interprets the .n2t file and finds the best match based on the connectivity information provided. See the many gmx-users mailing list posts in the archive about this topic. It's a frequently asked question. Unfortunately, the .n2t files are not well documented (this will be fixed in the next release) but I have posted very detailed instructions many times to the mailing list; Google is your best friend.
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