Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Timo Graen
On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: Hi GMX Users, please help me I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3. I am using AMBER99sb-ILDN force field and TIP4P water model. However, I am facing a problem in the ion adding step. when

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Mahboobeh Eslami
dear timo Please send me further details. I'm not a professional. Thanks and regards On Thursday, November 28, 2013 4:28 PM, Timo Graen tgr...@gwdg.de wrote: On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: Hi GMX Users, please help me I am trying to begin a simulation of a

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Mohsen Ramezanpour
Maybe you should modify your .tpr file manually according to what you added in the previous sections! On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: dear timo Please send me further details. I'm not a professional. Thanks and regards On Thursday,

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Justin Lemkul
On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: Maybe you should modify your .tpr file manually according to what you added in the previous sections! Manually modify a .tpr? How would one do that? The OP needs to provide the exact commands issued. The fatal error shown results from poor

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Mohsen Ramezanpour
Oh, I am sorry, I made a big mistake! :) Best Regards On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: Maybe you should modify your .tpr file manually according to what you added in the previous sections! Manually

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Mohsen Ramezanpour
Dear Justin I meant modifying .top file after adding some ions and water molecules which could be equivalent to -p option as you mentioned. What do you think about this? Please let me know On Thu, Nov 28, 2013 at 6:37 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Oh, I am

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Justin Lemkul
On 11/28/13 10:13 AM, Mohsen Ramezanpour wrote: Dear Justin I meant modifying .top file after adding some ions and water molecules which could be equivalent to -p option as you mentioned. What do you think about this? That would be one possible solution, but it is not yet clear what the OP