RE: AMBER: Xleap crash, problem with residue bonding

From: Ross Walker <ross.rosswalker.co.uk>
Date: Thu, 22 Jul 2004 14:31:22 -0700

Dear Armin,

I very briefly tried loading your lib file into xleap v8 and I do indeed
observe the same problem. I am not sure if this is a bug, a fundamental
problem in theory, or a problem with your lib file/system. It will take more
investigating. Something I have tried however is to comment out the warning
code so that xleap carries on running and does not abort when trying to
create the prmtop and inpcrd file. Interesting in this situation a prmtop
and inpcrd file are successfully saved (see attachment) but one is greeted
with the following warnings:

> saveamberparm te8 te8.prmtop te8.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
1-4: angle 191 210 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 191 210 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 191 210 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 153 172 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 153 172 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 153 172 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 115 134 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 115 134 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 115 134 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 77 96 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 77 96 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 77 96 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 22 77 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 22 96 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 25 78 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 25 79 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 25 80 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 25 97 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 25 98 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 25 99 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 39 115 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 39 134 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 42 116 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 42 117 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 42 118 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 42 135 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 42 136 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 42 137 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 56 153 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 56 172 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 59 154 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 59 155 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 59 156 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 59 173 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 59 174 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 59 174 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 59 175 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 73 191 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 73 210 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 76 192 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 76 193 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 76 194 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 76 211 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 76 212 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 76 213 duplicates bond ('triangular' bond) or angle ('square'
bond)
Building improper torsion parameters.
 total 24 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

So it seems that xleap thinks there are problems with certain angles
duplicating bonds that form a triangle (I guess). As you know your system
better than I do perhaps you could take a close look at these atoms and see
if you can see anything obviously wrong.

Also try the prmtop file I have attached and see if I works. I don't know if
it is missing any bonds or angles. Try running a short simulation with it
and visualise the results in VMD and see how you get on.

If you can't isolate the problem and can convince yourself that this is
probably a bug in xleap (it wouldn't be the first) let me know and I'll see
if I can investigate it further.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |
 

> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of opitz.che.udel.edu
> Sent: 22 July 2004 07:25
> To: amber.scripps.edu
> Subject: AMBER: Xleap crash, problem with residue bonding
>
>
> Dear Amber community,
>
> I am working with a star polymer that I am building in xleap,
> in Amber 7.
> I have defined the residues and they have worked in xleap before.
> When connecting the residues I xleap the following:
> tmp1 = sequence {cen arm1}
> set tmp1 tail tmp1.1.y
> tmp2 = sequence {tmp2 arm2}
> etc.
> When doing this the pdb as well as the results of an MD
> simulation viewed
> in MOIL-View had the residues NOT connected and they had
> drifted apart in
> the simultion.
> Therefore I tried to connect the residues by telling leap
> specifically to
> bond the atoms in question by using the bond command:
> bond tmp1.1.y tmp1.2.x
> bond tmp1.1.y tmp1.3.x
> bond tmp1.1.z tmp1.4.x
> etc.
> I am able to save the library file using the saveoff command
> (this file I
> will attach), but when I try to save the prmtop and inpcrd file using
> saveamberparm xleap crashes.
> It gives me the following error:
> !FATAL ERROR----------------------------------------
> !FATAL: In file [unitio.c], line 1763
> !FATAL: Message: 1-4: cannot add bond 25 77
> !
> !ABORTING.
>
> Can somebody please tell me what this error means and what I
> have to do
> differently to be able to save prmtop and inpcrd files from
> the lib file
> attached.
> Thank you very much in advance.
>
> Armin
>
> P.S.: The attached file is a *.lib file. This seemed to cause
> the e-mail
> to unsendable, therefore I just changed the file extension to
> *.out to be
> able to send it.
>
>
>
>



-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Thu Jul 22 2004 - 22:53:00 PDT
Custom Search