Hi,
You could also try the 'fixatomorder' command introduced with the
latest version of cpptraj. Example input:
parm outoforder.parm7
trajin outoforder.rst7
fixatomorder outprefix reorder
trajout reorder.rst7 restart
You should end up with two files with "fixed" ordering,
reorder.outoforder.parm7 and reorder.rst7.
-Dan
On Mon, Aug 19, 2013 at 6:35 AM, Thomas Evangelidis <tevang3.gmail.com> wrote:
> Hi Jason,
>
> It didn't work. I loaded the reordered .prmtop and .rst files in VMD and
> saw wrong bonding between the protein atoms. When I tried to run NPT
> equilibration using these files with pmemd.cuda I got:
>
> cudaMemcpy GpuBuffer::Download failed unspecified launch failure
>
> whilst with pmemd.mpi:
>
> | ERROR: PMEMD does not support intermolecular PRFs!
>
> I 'll send you my files to your gmail to see if you can find what's wrong.
> Just to tell you that I have followed the same protocol for another protein
> that differs only in one amino acid and worked perfectly fine.
>
> best,
> Thomas
>
>
> On 19 August 2013 04:03, Jason Swails <jason.swails.gmail.com> wrote:
>
>> On Sun, Aug 18, 2013 at 7:17 PM, Thomas Evangelidis <tevang3.gmail.com
>> >wrote:
>>
>> > Dear AMBER list,
>> >
>> > How do I get this error at unrestrained NPT equilibration since I can
>> load
>> > and visualize in VMD the prmtop and .rst file from NVT equilibration?
>> > The number of atoms in the .rst file is the same as in the .prmtop. Below
>> > is the configuration file I used in NVT.
>> >
>>
>> This is a bug in tleap that results when you combine two separate molecules
>> using the 'bond' command in tleap. It is a bug in tleap that is known, but
>> has not yet been fixed.
>>
>> There is a relatively simple workaround in either cpptraj or ParmEd (make
>> sure you have AmberTools 13 fully up-to-date).
>>
>> Using ParmEd, try this:
>>
>> parmed.py -p <your_prmtop> << EOF
>> loadRestrt <your_restart>
>> setMolecules solute_ions True
>> parmout <reordered_prmtop> <reordered_restrt>
>> EOF
>>
>> reordered_prmtop and reordered_restrt should then work.
>>
>> The error, in case you are curious, is that the SOLVENT_POINTERS and
>> ATOMS_PER_MOLECULE sections of the prmtop are structured under the
>> assumption that all of the molecules are composed of consecutive atoms.
>> However, if molecules 1 and 3 are combined via a 'bond' command in tleap,
>> then the atoms are not properly reordered to satisfy this assumption. This
>> results in a broken ATOMS_PER_MOLECULE section of the prmtop which can
>> later result in very strange errors (e.g., segfaults) in sander and pmemd.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Aug 19 2013 - 12:30:03 PDT
