[gmx-users] protein simulation w/ urea + water

2011-07-20 Thread E. Nihal Korkmaz
Dear all, I am trying to simulate a protein in urea solution. I used *genbox -cp protein_in_box.gro -cs urea+h2o.gro -o out.gro -p topology* but the resulting topology doesn't contain any information on urea nor the atoms of urea. I also tried adding ureas on the protein with *-ci urea_single.gro

Re: [gmx-users] protein simulation w/ urea + water

2011-07-20 Thread Justin A. Lemkul
E. Nihal Korkmaz wrote: Dear all, I am trying to simulate a protein in urea solution. I used /*genbox -cp protein_in_box.gro -cs urea+h2o.gro -o out.gro -p topology*/ but the resulting topology doesn't contain any information on urea nor the atoms of urea. I also tried adding ureas on the

Re: [gmx-users] protein simulation

2009-12-28 Thread Mark Abraham
edmund lee wrote: Dear all, I am trying to do a simulation of protein OMPA. At the step grompp, it shows a fatal error stated Fatal error: Atomtype 'HC' not found! I tried to configure the error but i failed. So, hope that anyone can help me in this. There are various underlying causes.

[gmx-users] protein simulation

2009-12-27 Thread edmund lee
Dear all, I am trying to do a simulation of protein OMPA. At the step grompp, it shows a fatal error stated Fatal error: Atomtype 'HC' not found! I tried to configure the error but i failed. So, hope that anyone can help me in this. Thnaks..