Re: Help! unstable simulation - ARG go nuts...

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Dec 16 2003 - 22:10:31 CST

Hi,

It looks like this is your problem:

unknown patch type PT1
ERROR: failed to apply patch

(Yes, psfgen should really crash and burn here...)

I think you meant to type TP1. If you do, you get:

applying patch TP1 to 1 residues
unknown atom type ON3
add atom failed in patch TP1
ERROR: failed to apply patch

Your top_PTR.inp file contains the following note:

! this patch requires that the use of the following
!
!1) protein topology file that contains mass list of atoms in both
! the protein and nucleic acid topology files and
!
! add to the topology file
!MASS 179 ON2b 15.999400 ! Nucleic acid phosphate ester oxygen (pres
tp1/tp2)
!
!2) parameter file that contains both the protein and nucleic acid
! parameters plus the parameters listed below

If I substitute the prot_na topology file for prot_lipid there are other
atom types missing, but if you include them both then psfgen is happy.

Hopefully this will fix your minimization problems.

-Jim

On Tue, 16 Dec 2003, Gadi Oron wrote:

> Hello,
>
> On Fri, 2003-12-12 at 11:16, Alexandre Vakhrouchev wrote:
>
> Thank you for your reply.
> >
> > First of all look at the output of your psfgen script (it is attached
> > as 'pfs.log').
>
> I have noticed that some coordinates are guessed, but I don't think that
> this is the reason for the crash. You are right though that the the
> crash is due to close atoms, I have written a script that finds atoms
> too close to each other, and found that at the end of the minimization
> some atoms are literally on top of each other. The problem is that this
> was not the case before the minimization! ARG residues are especially
> bizarre. Their atoms simple collapse during minimization to distances
> less than half an A(!!). I have attached a snapshot to illustrate it.
>
> I do believe that this in NOT due to the patches that I apply since
> before minimization everything is fine. I have also isolated a single
> chain that is not patched or modified, and it behaves the same (chain
> C).
>
> The only way I could get the dynamics running is to specify
> "exclude none", but in this case the protein swells into unrealistic
> dimensions (H bonds become 2A long!)...
>
> Any ideas?
>
> > I solved this error by providing coors for all atoms,
> > depending on Rmin/2 values (from Van-der-Waals force field
> > parametres), but i had to
> > write additional programm.
>
> I would be glad to have this prog... even though I doubt it would be of
> great help...
>
> Thank you for your help.
> --
> ================= Gadi ORON, PhD -o- Proteologics ======================
> =========== gadi/at/proteologics.com =========== +972 8 9475666 ===========
> Also, the Scots are said to have invented golf. Then they had
> to invent Scotch whiskey to take away the pain and frustration.
>

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