Hi,

In this case, the input structure to pdb2gmx has hydrogen atoms whose naming differs from that given in the .rtp file of the force field.

The .rtp file contains amino acid specific information - the atoms that constitute it, their charge (masses are retrieved from the atomtypes.atp file using the atom name) and the bonded potentials (bond, angle, dihedral, impropers) used to model the amino acid. The coordinates in the pdb file along with the cognate force field information in the .rtp and ffnonbonded.itp files contain all the information required to start a simulation.

This specific naming convention is what gromacs expects when it encounters a given amino acid in a pdb file. As the input in this case does not comply with this, pdb2gmx throws an error.

The hydrogen atoms in the input structure can be ignored by using the -ignh flag of pdb2gmx. If this flag is used, the positions of the hydrogen atoms to be added will be guessed by pdb2gmx. If the hydrogen positions need to be retained, the names in the input pdb file must be changed to match those in the rtp file.

Hi,

In this case, the input structure to pdb2gmx has hydrogen atoms whose naming differs from that given in the .rtp file of the force field.

The .rtp file contains amino acid specific information - the atoms that constitute it, their charge (masses are retrieved from the atomtypes.atp file using the atom name) and the bonded potentials (bond, angle, dihedral, impropers) used to model the amino acid. The coordinates in the pdb file along with the cognate force field information in the .rtp and ffnonbonded.itp files contain all the information required to start a simulation.

This specific naming convention is what gromacs expects when it encounters a given amino acid in a pdb file. As the input in this case does not comply with this, pdb2gmx throws an error.

The hydrogen atoms in the input structure can be ignored by using the -ignh flag of pdb2gmx. If this flag is used, the positions of the hydrogen atoms to be added will be guessed by pdb2gmx. If the hydrogen positions need to be retained, the names in the input pdb file must be changed to match those in the rtp file.

Thank you sir

I have another clarification,  In the grompp creation of ion.tpr files.  Fatal error is too many warnings (1) and grompp terminated.

asking to use -maxwarn option , how to use it and if i use this it asking for argument. could you solve this problem.

Hi,

Warnings given by gromacs indicate some important issue. If you think that it is fine to proceed, then use the -maxwarn flag. The argument is the number of warnings that you want grompp to overlook, in this case 1 (-maxwarn 1)

To get a better idea of the whole process of setting up simulations, you can look at the following tutorials by Dr. Justin Lemkul.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/

Thank u sir

Hello Atul,

What can I do if the problem of atom is about carbon? I redefined the atoms and checked there is no mismatch between them. The gromacs still give me this error when I tried to convert pdb file using gmx pdb2gmx just like Malathi I assume. The error is following:

Atom CT3x in residue EthB 1 was not found in rtp entry EthB with 7 atoms

while sorting atoms.

Ps. I tried to use Gromacs for polymers and the residues are not standard protein residue but defined as building blocks.

Hi guys,

I have the same problem,

This is my command:

gmx pdb2gmx -f 1gzx.pdb -o 1gzxH.gro -water none -ff oplsaa

And this is the error I get:

Atom ha3 was not found in the entry with 9 other atoms

I used -ignh but I received new errors.

What do you recommend?

+

I also receive an error for this command:

gmx pdb2gmx -f 1gzx.pdb -o 1gzxH.gro -water none -ff oplsaa

error: atom N not found in building block 1ACE while combining tdb and rtp

This is one of the advices I got from net (Thanks to Justin Lemkul):

Nowhere in the explanation of the error does it suggest that you should alter the .rtp file in this instance. You have atoms in your structure that are not in the .rtp entry. Specifically, your structure file has an N atom in ACE, but ACE only contains CA, C, and O. The N atom should be the first atom in the next residue, not ACE.

But I have no idea how to deal with this problem. Because it just explains the issue without any solution.

Yes that is the reason for it but how to make the naming of H atoms in both the input protein and rtp files as same?

I had the same problem,

I just remodelled the protein using modeller, and energy minimized the protein using CG method for 1000 steps, and it works just fine in gromacs.

Use -ignh flag in the command. To avoid hydrogen. Specifically running with all atom force field. This is a common message

Ajay Yadav Atul Kaushik Rangadurai will using ighn flag cause any error??