Hi,
On Mon, Oct 5, 2015 at 1:15 PM, Osman, Roman <roman.osman.mssm.edu> wrote:
> No fix yet, I assume.
I'm not sure what 'fix' you are referring to. The 'fixatomorder'
command *is* the promised fix in these emails:
http://archive.ambermd.org/201409/0451.html
http://archive.ambermd.org/201307/0430.html
The issue is that when you modified your original topology and
trajectory you were left with molecules with non-consecutive atom
ordering (likely due to the disulfide bond). Programs in Amber by and
large operate on the assumption that atoms in residues and molecules
are consecutive; when this is not the case unexpected behavior can
happen, which is why the error message pops up in the first place.
Hope this helps,
-Dan
>
>> On Oct 5, 2015, at 3:09 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> Why not use the 'fixatomorder' command in cpptraj to fix your topology
>> and trajectory, then run MMPBSA.py using the reordered
>> topology/trajectory? E.g.,
>>
>> parm myparm.parm7
>> trajin mytraj.nc
>> fixatomorder outprefix reordered
>> trajout reordered.nc
>>
>> -Dan
>>
>>
>> On Mon, Oct 5, 2015 at 12:51 PM, Osman, Roman <roman.osman.mssm.edu> wrote:
>>> Hello,
>>>
>>> I have an “artificial” molecule, which was obtained by removing portions of the original one in order to enhance the calculations in MMPBSA. In the complex and the receptor there is a disulfide bridge between CYX residues in different chains. All seems to be OK until I run the MMPBS.py where I get the error listed above.
>>> Atom 1512 is in the chain that contains the second CYX.
>>>
>>> I read the archive discussion https://urldefense.proofpoint.com/v2/url?u=http-3A__archive.ambermd.org_201409_0451.html&d=AwIGaQ&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=bgoO3S4pwgB7LIziZ_2pbcRaMqElSi9zluAnGVe3dZk&s=la64jSjHWav254izo3ku6GUfo9nnq7exjHfhm5GKYxQ&e= but there it does not offer a solution for running MMPBSA.py, rather it offers a solution in cpptraj.
>>> There is also a promise for a fix.
>>>
>>> Could you suggest what to do.
>>>
>>> Thanks for your help
>>> Roman Osman
>>> Department of Structural and Chemical Biology, Box 1677
>>> Mount Sinai School of Medicine
>>> New York, NY 10029
>>> roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=AwIGaQ&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=bgoO3S4pwgB7LIziZ_2pbcRaMqElSi9zluAnGVe3dZk&s=_ivScElRiWAs1VQ2iO72hnzr5bR5MIAQhWTe4mQeIf4&e=
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__home.chpc.utah.edu_-7Echeatham_&d=AwIGaQ&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=bgoO3S4pwgB7LIziZ_2pbcRaMqElSi9zluAnGVe3dZk&s=SSdMEWyCYfLaRqI05tofygzk955Ej7xfecuz--3ZWbY&e=
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=AwIGaQ&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=bgoO3S4pwgB7LIziZ_2pbcRaMqElSi9zluAnGVe3dZk&s=_ivScElRiWAs1VQ2iO72hnzr5bR5MIAQhWTe4mQeIf4&e=
>
> Roman Osman
> Department of Structural and Chemical Biology, Box 1677
> Mount Sinai School of Medicine
> New York, NY 10029
> roman.osman.mssm.edu
>
>
>
> _______________________________________________
> 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 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 05 2015 - 13:00:03 PDT
