[gmx-users] Error in top when using oplsaa with tip4p

Dear colleagues, I carried out successfully an MD simulation of a protein in water using the GROMOS 96 force field with spce water. But I have a problem in switching to OPLSaa. I proceeded as usual: # pdb2gmx -ff oplsaa -f pn.pdb -o pn2.pdb -p pn.top -his -ss -water tip4p # editconf -bt oct

[gmx-users] Exclusions for aromatic residues

Hi, In .rtp file of a GROMOS 96 force field (ffG43a1.rtp for example), exclusions seem to be listed only for aromatic residues such as TYR, HIS, and TRP. Why is that so? Sanghwa Han ___ gmx-users mailing listgmx-users@gromacs.org http://www.gro

RE: [gmx-users] Format of a Topology File When Using Amber FF inGromacs

: Tuesday, June 19, 2007 4:31 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Format of a Topology File When Using Amber FF inGromacs 한상화 wrote: > Dear Gromacs users, > > > > I have successfully installed Amber FF in Gromacs according to the > instruction

[gmx-users] Format of a Topology File When Using Amber FF in Gromacs

Dear Gromacs users, I have successfully installed Amber FF in Gromacs according to the instruction by the Pande Group (http://folding.stanford.edu/ffamber/). I ran a demo successfully and enjoyed the speed of Gromacs. My questions are: [Question 1] The topology file produced by pdb2gmx with

[gmx-users] LINCS error during mdrun

Dear GROMACS users, I am trying to run md of a protein with a non-standard residue. It was fine up until I ran mdrun with pr.mdp, where I received a LINCS warning after 20 steps (0.042 ps). Step 21, time 0.042 (ps) LINCS WARNING relative constraint deviation after LINCS: max 23696503603

RE: [gmx-users] Disulfide between protein Cys and GSH

MACS users Subject: Re: [gmx-users] Disulfide between protein Cys and GSH 한상화 wrote: > Thank you Mark. > The method you suggest is exactly what I tried. > I prepared a structure of two molecules in which the S...S distance was > made to be 0.206 nm (this value is within the tolera

RE: [gmx-users] Disulfide between protein Cys and GSH

intermolecular disulfide. Sanghwa han -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Wednesday, January 17, 2007 3:09 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Disulfide between protein Cys and GSH 한상화 wrote

RE: [gmx-users] Disulfide between protein Cys and GSH

flag for this purpose). Thanks -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Wednesday, January 17, 2007 2:19 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Disulfide between protein Cys and GSH 한상화 wrote: > D

[gmx-users] Disulfide between protein Cys and GSH

Dear all, Is there any way to make a disulfide between protein CysSH and GSH? Or an interchain disulfide? I am interested in running MD for Protein-S-SG (i.e. glutathiolated protein). Thanks Sanghwa Han ___ gmx-users mailing listgmx-user

[gmx-users] Error in .top when running grompp for final product MD

Dear gromacs users, I am running MD for a protein with 212 amino acid residues. When I run grompp (grompp -f pn_md.mdp -c pn_md.pdb -r pn_md.pdb -p pn.top - o pn_md.tpr ) for the final product MD, I receive the following error message. I properly included sol and ion in the temperature contro

[gmx-users] Error in .top file for grompp

Dear Gromacs users, I have gone through all the way to the final product MD, where I received the following error message for grompp. The same topology file pn.top did not give me any problem in the previous steps including grompp with pr.mdp or grompp with em.mdp. I included solvent and ions