I did the exercise as you said. A .pdb file of ACE and VAL. I ran the pdb2gmx, entered none as the N-terminus and COO- as the C-terminus. The atomtyps that charmm selects for the acetyl is as below: 1 CT3 1 ACE CH3 1 -0.27 12.011 ; qtot -0.27 2 HA 1 ACE HH31 2 0.09 1.008 ; qtot -0.18 3 HA 1 ACE HH32 3 0.09 1.008 ; qtot -0.09 4 HA 1 ACE HH33 4 0.09 1.008 ; qtot 0 5 C 1 ACE C 5 0.51 12.011 ; qtot 0.51 6 O 1 ACE O 6 -0.51 15.999 ; qtot 0 I thought that when H is instead of CH3 group, I will have a C atom of type CT1 in formyl.
But when I entered the grompp command I got 13 errors as kind of the errors got befor ( no default bonds or... ) What do you suggest me? Any other homework to do? I will do! Sincerely, Shima ----- Original Message ----- From: Shima Arasteh <shima_arasteh2...@yahoo.com> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Sunday, July 29, 2012 2:44 PM Subject: Re: [gmx-users] Diagnosing + system blowing up Uh-huh.................. :-) ;-) I visualized the .pdb in VMD and it seems OK. All right, I will do the exercise for tonight. :-) Thanks Mark. Sincerely, Shima ----- Original Message ----- From: Mark Abraham <mark.abra...@anu.edu.au> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Sunday, July 29, 2012 6:54 AM Subject: Re: [gmx-users] Diagnosing + system blowing up On 29/07/2012 4:47 AM, Shima Arasteh wrote: > > > Dear Mark, Thanks for your suggestions. > Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is > tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all! Uh-huh... there's a known initial issue with a bond between 18 and 1 and later issues with 1-4 interaction between 5 and 1... and now you think there is a bond from 18 to 5? This makes no sense. > However I see this pair in the [pairs] section of topology ! > So I can get the result of an inappropriate bond interaction here! Correct? > Now I think it's not necessary to go through the diagnosing steps any more! > :-( > What is my duty right now?! > > Is this problem supposed to be fixed in the .pdb file? What's wrong with the > pdb file? What about erasing the unexpected bond interactions in topology > file? As I've said, at least one of your topology and initial coordinates don't make sense. If you visualize the coordinates and they make sense, then you need to go back and get a proper topology, like Justin said. Blindly erasing interactions is ineffective. Go and design it properly, probably from the beginning or from what Justin said. As an exercise, get a simulation of Val with acetyl and some C-terminal capping residues working. Then work out from that example how to define and use an .rtp entry that is acetyl-Val. Then adapt that to formyl-Val. Mark > > > Sincerely, > Shima > > > ----- Original Message ----- > From: Mark Abraham <mark.abra...@anu.edu.au> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Cc: > Sent: Saturday, July 28, 2012 7:15 PM > Subject: Re: [gmx-users] Diagnoding + system blowing up > > On 28/07/2012 9:34 PM, Shima Arasteh wrote: >> Hi all, >> >> My system has got BLOWING UP . I followed the protocol in >> http://www.gromacs.org/Documentation/Terminology/Blowing_Up and got as below: >> >> Step 1: If the crash is happening relatively early (within a few steps), set >> nstxout (or nstxtcout) to 1, capturing all possible frames. Watch the >> resulting trajectory to see which atoms/residues/molecules become unstable >> first. >> I got this warning: >> Warning: 1-4 interaction between 5 and 18 at distance 2.003 which is larger >> than the 1-4 table size 2.000 nm > Classic symptom of blowing up, and much more so than all of the other > problems you reported. Please get in the habit of reading all the output > before reaching conclusions ;-) > >> Step 2: Simplify the problem: >> If you have a new box of solvent, try minimizing and simulating a single >> molecule to see if the instability is due to some inherent problem with the >> molecule's topology or if instead there are clashes in your starting >> configuration. >> >> I got this: >> Now there are 24 residues with 360 atoms >> Making bonds... >> Warning: Long Bond (1-18 = 0.357049 nm) > So you were ignoring warnings from pdb2gmx...? There's a lesson there - > everything you've done after ignoring that was doomed to fail. It can be > right to ignore a warning, but you should know why it is right. If your > topology defines a bond between atoms that are 0.35nm apart in your starting > configuration, then either your topology or configuration have a serious > problem. > > So satisfy yourself whether there should be such a bond in the topology, or > whether the starting geometry is silly. > >> Step 3: Monitor various components of the system's energy using g_energy. >> If an intramolecular term is spiking, that may indicate improper bonded >> parameters, for example. >> >> The improper-dihedral plot is strange. It "goes up in first picoseconds" and >> then goes down slightly. > Sure, you probably have some inappropriate bond interaction, so something has > to give. The thing that looks weird is not necessarily the cause of the > problem, though... > >> I think there is something wrong in dihedrals which I defined in .rtp file >> in the new residue. atom 18 is the H atom of formyl ( Formyl is as the >> N-terminus and is connected to a Valine residue) > And atom 1 or 5 is...? Does that make sense? > > Mark > >> Now , what do I need to do? Going to the next step of diagnosing? or no? How >> can I fix the problem? >> >> Would you mind helping me please and give me suggestions? >> >> Thanks in advance. >> >> Sincerely, >> Shima > -- gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? 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