I am trying to simulate how crystallization of glucose monohydrate takes place. I have created glucose monohydrate pdb file and was using GROMOS 53a96 forcefield. when i start with pdb2gmx program to obtain the topology, it ends with an fatal error stating GLC not found in rtp entry while sorting atoms.
similar research was done in following articleArticle Chemical and molecular dynamics analysis of crystallization ...
CAN ANYONE PLEASE PROVIDE ME PROCEDURE OR PROVIDE ME THE FILES REQUIRED TO CARRY OUT THE SAME FOR GLUCOSE ?
Rishi Naik
The error states that the three letter code GLC is not found in the topology of GROMOS 53a96 forcefield.
You can open the respective topology file of force field and check whether glucose has built-in topology. if so, what is the respective three letter code
if not, you need to create toplogy with 'topology builder tools' like ATB, SwissParam and integrate the topology
Doing google will give enough idea to troubleshoot
Hope it helps
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