[gmx-users] pdb2gmx -ss option

Dear all, I'm using the old 3.3.3 version of gromacs and I try to use the -ss option of pdb2gmx to select interactively the ss bridge in my protein. But I don't remark any change between using -ss option and not using it. The -inter option give me some interactive options such as lys or arg but

Re: [gmx-users] pdb2gmx -ss option

Thank you for your response. I use 3.3.3 version because it's this one which is installed on the cluster, and that is difficult to change it without causing any bug and a reviewing is in process for the webservice. So change it now should be difficult. To be able to select cysteins with the -ss

[gmx-users] grompp g96angle types error

Dear all, I launch those commands for few models : pdb2gmx -f 2it7-10_bestene1mc-SC.pdb -o 2it7-10_bestene1mc-SC.gro -p 2it7-10_bestene1mc-SC.top -ignh -missing editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0 -c -bt cubic grompp -c 2it7-10_bestene1mc-SC-box.gr

Re: [gmx-users] grompp g96angle types error

The problem seems to be between 3 S of CYS residues. I only use the 20 usual residues and with no modifications. Where is the ffbonded.itp file? Thank you, Pierre THEVENET - Mail original - De: "Justin A. Lemkul" À: "Discussion list for GROMACS users" Envoyé: Mardi 17 Janvier 2012 1

Re: [gmx-users] grompp g96angle types error

Ok! The problem doesn't really come from gromacs so. It's my side-chain positioning software which made this... I'll try to fix it. Thank you very much. Pierre THEVEVENET - Mail original - De: "Justin A. Lemkul" À: "Discussion list for GROMACS users" Envoyé: Mardi 17 Janvier 2012 15

[gmx-users] pb2gmx SS bond selection

Dear all, I'm using the option -ss to select the SS bonds I want to preserve when so problem occur with multiple bonds possible. The problem is that pdb2gmx asks me if I want to preserve the bound between an atom or not. It is very difficult to do this automatically. Is there a way to tell pdb2g

[gmx-users] SS bond forcing

Dear gmx users, I try to use gmx to make some minimization. Unfortunatly, I have some SS bonds which are not formed in my PDB because the S-S atoms are too far away to connect to each other. I saw at that page : http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds that it is pos

Re: [gmx-users] SS bond forcing

Here is what I have done: First, I created the .gro file with the command line: pdb2gmx -f test.pdb -o test.gro -p test.top -ignh -missing Then, I added at the end of my test.top file the following lines (I double checked the atom numbers): [ distance_restraints ] ; ai aj type index typ