Dear all
I have to simulate a protein-drug complex in GROMACS. for protein I have used Amber99SB-ildn. and for drug I used GAFF. however grompp says "Atomtype c3 not found" which is SP3 carbon of ligand. Please suggest how can I fix this problem.
thanks in advance
Surya
Dear Surya
Atomtype that is indicated in topology has to match atomtype in .gro file. I thinks therefore it is going wrong. Adapt atomtypes in .gro exactly like in topology. Then it should be ok.
Dear Jam
Many thanks for the suggestions.
I could fix atom types with help of old discussions in gromacs mailing list. here are those links which may be useful for many others.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-April/088427.html
http://permalink.gmane.org/gmane.science.biology.gromacs.user/41033
Dear Surya,
How you reassigned the atomname for c3 ? I my case, I was stuck in similar problem, when I examined the atomtypes, I found the carbon in -CF3 was named as c3. I changed it to C and it worked. I don't know whether this method is correct or wrong. It seems from old discussions that we have to add these new atom types in AmberFF.
Dear Rakesh
c3 means sp3 hybrid carbon. In gromacs it is defined by "CT". For more details please follow links given in above reply.
Dear surya ,
I am also facing same type of problem. I read the above given link but i did not found any relevant answer. Can you suggest me. How can i solve my problem.
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology