Ligand topology with gromacs
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4.6 years ago
kh.amine1 • 0

I have to simulate a big complex with two different proteins, GNP ligand and acetate(ACT), MG and CA ions.

I’m using gromacs software and amber force field to generate the topology for the protein.

I have faced a first issue regarding ACT ion and GNP ligand because they are not found in residue topology database. But I guess AMBER supports this molecule inherently.

For that, I have used PRODRG program to generate the GNP topology first and I have followed the same procedure as explained in Benvan Lab tutoriel.

The structure I got from this phase is good but when I tried to superpose the GNP with my reference structure it seems that the built GNP coordinates are not the same. The GNP is translated.

My first question is: is PRODRG the suitable program for generation of small molecule topologies?

Should I look at the atomic charges obtained with PRODRG for GNP before merging it with the protein?

Could any on, please, suggest me other ways to succeed this critical phase.

Grateful!

sequence software error • 3.1k views
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4.6 years ago

My first question is: is PRODRG the suitable program for generation of small molecule topologies?

No. please use acpype webapps.ccpn.ac.uk/acpype/ ) or better use ATB (https://atb.uq.edu.au/ only gromos forcefield). For complete list see:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html

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Thank you very much for your reply.

I installed ACPYPE as you suggested and the other amber tools.

Unfortunately, once I run the command *acpype –i ligand.pdb * I got this error:

==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'ligand2_AC.prmtop'

I tried to write prmtop using Chimera and assign charges to the ligand but I got error: Faillure running ANTECHAMBER for ligand

Do you know about the problem?

Thank you again

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Anyone to help.

I need your suggestions and comments!

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The ligand of the protein am using is GNP.

I think, it's a molecule classified as non-standard residue.

In that case, how canI write its topology?

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