I am trying to modify a pdb file (of a system designed in Materials Studio), in such a way that it is coherent with GLYCAM force field parameters in Amber.
- Is it ok to use any residue name I get from "list" of loaded GLYCAM in tleap? does it make a different what residue name I use?
- How should I change the atom names to ones that are understandable by Amber? I mean, to what name a carbon atom called e.g. C12 in my original pdb should changed? I can see a list of atoms in the library files of e.g. GLYCAM_amino_06j-12SB.lib. but which one is coherent with C12 let's say?
Thank you in advanced,
Ali
Before importing the pdb file in Amber, change it's format by "pdb4amber" script of Amber.
About the GLYCAM force field, there's only one standard type of GLYCAM in Amber force field - If your system is not involved in it, you may define a new force filed for that. Yes it's challenging and decreases the accuracy.
apparently, what pdb4amber does is only changing the file in such a way that it is readable by amber, yet amber cannot recognize the residue and atom names afterwards. My point is, how to change it so that it is coherent with amber libraries?
If your system involves non-standard residues, you may search in the amber force fields to find equivalent potentials for your systems - for non-standard residues there's not any automated way for generating input file; as I mentioned in my previous post, it's challenging.
If your system is small in size, Amber General force field may be helpful.
Thank you Ramin. I solved the problem by modifying the residue names into standard amber ones, as well as the atom names. The system consists of 5300 atoms. The only problem now is that it consists of only one type of residue while atoms are repeating in the model. Atoms in each residue should be unique. I can use letter indicators for the residues (A-Z) to separate them but there are around 180 residue groups, while there is only one column dedicated to the residue indicators. Do you have any idea how to solve this?
The atom types can be repeated to get potential from force field - but the atom numbers are not.
Atom number is different from Atom type. Force field does not sense the atom number.
I believe this is not correct, as amber complains when atom names are repeated within a residue, that is why changing the residue indicators and residue sequence number can be a solution to tackle this problem when it comes to systems with repeated units.
Following are the two warnings I was getting, leading to fail in generation of the topology files. However, the problem was solved by the explanations above.
Warning: Atom names in each residue should be unique.
(Same-name atoms are handled by using the first
occurrence and by ignoring the rest.
Frequently duplicate atom names stem from alternate
conformations in the PDB file.)
Warning: Unknown residue: MOL number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
Can anyone tell me how to get mol2 file for amber? which include atom types. my file contain 2000 atoms and it is graphene oxide sheet
Nikhil Maroli A simple way is to upload the PDB file in VMD and save the coordinates in mol2 file type. Have you tried this yet?
Hi,
Can anyone tell me how can I change the Atomname in a system.gro file using gromacs command. Like I want to change CA to CB.
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