Shen,

Your model 3HBT is protein in complex with ATP, sulfate ion and calcium ion. Moreover it also contain one of the modified aminoacid residue (HIC). Most probably it is on of the state of histidine. You better check it out. Technically, your pdb file contain non standard residues. And you need to parametrize those residues before you generate PDB+PSF pair.  In simpler words, Your VMD can only generate PSF for residues that are already known in the topology file. And these nonstandard aminoacid residues are not described in the topology file you are using. Hence it complains about presence of "unknown atom type"  Therefore you shall have to first generate its topology. and then you need to parametrize the novel residue before you begun your simulation.

Hopefully it helps.

Cheers for VMD!!

It seems that you have included a proper pdbalias for HIC. And it seems that VMD is not able to take care of one of the oxygen (OG2P1) from sulfate ion.

Meshram,

Thank you for your reply!

I will try to parametrize residue of protein and generate the topology file of the residue. But I have an another problem about the topology file.  How can I generate the topology file by myself?

About the HIC, thank you for your remind!

I tried to use a new  topology files ( top_all36_cgenff.rtf, top_all36_prot.rtf, so4.rtf and atp.rtf) today. These file were made by  CHARMM-GUI (http://www.charmm-gui.org/?doc=input/pdbreader). Lucky, I could get the psf file. However, it could not work in NAMD when I try to minimize energy. So, I think I must generate topology file about the residue.

Best Regard.

Cheers for VMD!

Try out Paramchem at https://cgenff.paramchem.org/userAccount/userLogin.php Register there first, its free and you can generate topology as well as parameter files for any non standard residues that are compatible with NAMD. I use the same server for parametrizing new compounds for our medicinal chemistry division.

Dr. Meshram,

I really appreciate you for your answers!

According your advice, I can get the psf file sucessfully!

Good Luck!

The topotools plugin of vmd can be used to write out psf files for any pdb file. It works if you know the charges of the individual atoms/united atoms and also the atom types to link with the parameter files. Here is a detailed tutorial:

www.lennardjones.com/karp/namd/psf2.html

Hello, I can see that this post is old but I have a similar question.

I want to use CHARMM-GUI to generate a PSF file of my complex.pdb (complex=protein.pdb+two ligands-reference and mutant in one file).

As you explained I will need the common topology for the two ligands since CHARMM doesn't have it. Can CHARMM-GUI create an rtf file, which will contain the two ligands? Or should I do that manually?

I go to Quick MD Simulation, upload my complex.pdb file,

select the chains of the protein + the ligands

select "Reading Hetero Chain Residues" - "Use CHARMM General Force Field to generate CHARMM top & par files" - "the SDF file from RCSB" but in the end the atoms of my reference ligand do not exist in the PSF file. I am I missing something?

Alternately, instead of "Use CHARMM General Force Field to generate CHARMM top & par files" I can use "Upload CHARMM top & par for hetero chain" to actually give the topology needed, but how can I create that file?

Thank you,

Matina