[gmx-users] Aminoacids.hdb problem

*Dear gmx-users, I am trying to insert a custom residue (a phosphoserine) in Gromacs using force field Amber ff99sb-ildn. I created a new .rtp entry named SEP like this:* [SEP] [ atoms ] NN -0.49370 1 HH0.30180 2 CA CT -0.23800 3

[gmx-users] Pdb2gmx with Amber99SB-ILDN

Dear gmx-users, I encountered a problem using pdb2gmx with Amber99SB-ILDN when I tried to use the -ter flag in order to select "none" as termini state. Pdb2gmx simply ignores -ter, and doesn't prompt the list of entries for termini selection. Has anyone else had this kind of problem? Alberto --

[gmx-users] -ter flag, pdb2gmx

Dear gmx-users, I'm having some problems using the flag "-ter" of pdb2gmx. The syntax I'm using is the following, for a protein dimer: pdb2gmx -f protein_dimer.pdb -o start.gro -p start.top -ter Instead of prompting a menu with the choice of different c

[gmx-users] Disulphur bridge parameters

Dear gromacs users, I am simulating a protein complex with a disulphur bridge. I put the two chains in the same "moleculetype" definition, and through pdb2gmx I generate the disulfur bridge. When I checked the .top file for angles and dihedral angles potential parameters I found out that these fiel

[gmx-users] Thioester bond problem

Dear Gromacs users, I'm attempting to simulate a system composed of two proteins containing a thioester bond between the C-terminus of chain A and a cysteine residue from chain B. I wonder if the parameters for this bond to be included in the .top file exist. Also, I am having troubles figuring out