Thanks
No fix yet, I assume.
> 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>
>>
>>
>>
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>
>
>
> --
> -------------------------
> 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
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>
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> 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
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Received on Mon Oct 05 2015 - 12:30:05 PDT
