Hi, Roman
First, the NFE cannot be used for minimization (imin=1). However, always
the minimization will not change the system too much. So you can still
add the restraint when running equilibrium run.
If you are using pmemd.cuda, update your Amber16 with new patches. And also
download a ThirdParty patch here, apply it and recompile.
https://github.com/pfreezer/AmberPatch
You should add another &pmd section in you mdin file, check the updated
manual and the README in my patch. Basically you need
anchor_position = r1, r2, r3, r4
anchor_strength= k1, k2
to tell Amber the restraint
for the CV part, you are almost OK, but you should put it a separate file,
and cv_i can not be in the format 973:7377, you should
write all the atom ID explicitly, like 973, 974,... 7377. I know this is
boring and make the cv file too long but now this is only code can read. A
little scripting should
make this not too hard and also you may just account for the heavy atoms.
cv_r is no use here, you can leave it.
Tell me if you still can not run it.
Best
Feng Pan
On Wed, Feb 15, 2017 at 2:34 PM, Osman, Roman <roman.osman.mssm.edu> wrote:
> Hi Adrian,
>
> Yes, I am using amber16 that was installed and tested in August 2016.
>
> Rami
>
> On Feb 15, 2017, at 2:31 PM, Adrian Roitberg <roitberg.ufl.edu<mailto:
> roitberg.ufl.edu>> wrote:
>
> HI
>
> What version of amber are you using, and if 16, does it have all patches
> applied ? The nfe syntax has changed recently
>
> Thanks
>
>
>
> On 2/15/17 2:29 PM, Osman, Roman wrote:
> Hello,
>
> Perhaps someone can help in constructing the input for doing simulations
> in amber using a radius of gyration constraint.
>
> I have a peptide embedded in a micelle of about 100 DPC that was
> constructed in PACKMOL and then the entire system was placed in a periodic
> box with waters and ions. I would like to minimize and equilibrate the
> micelle so all the polar groups are on the outside layer of the micelle
> facing the water. It seemed to me that applying a radius of gyration
> constraint on the N atoms of the DPC would be the correct way.
>
> The manual is not clear of how to prepare the input. One version of it is:
> Minimization input file in explicit solvent
> &cntrl
> ! Minimization options
> imin=1, ! Turn on minimization
> maxcyc=5000, ! Maximum number of minimization cycles
> ncyc=2500, ! 100 steepest-descent steps, better for strained
> systems
> .
> .
> .
> owtnm='OH2', ! Water oxygens are named OH2
> /
> Protein posres
> 10.0
> RES 1 62
> END
> END
>
> variable
> type = R_OF_GYRATION
> i = (973:7377)
> r = (21.5)
> end variable
>
> But the last part is apparently not read. Moving it to the &cntrl section
> produces a read error.
>
> I found an update (from 2012?) that suggest a different form:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.
> org_doc12_nfe.pdf&d=DwICAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=q8vs_
> fbTOEJjOKNIgjun94sbqYxVkxfOTdUE1xTyUk0&m=a72u5PCYwCzVD_
> CKyOufEIAXZaiDXLmwhiNBH7v-Xho&s=0M7W0jjdhM_ol7qWQE_
> W5aqdAbMy6WUHqzA3AuOnyY8&e=
>
> which I added to the input but placing it inside the &cntrl section does
> not work and outside it seems not to be read.
> Here is the form:
>
> &colvar
> cv_type = R_OF_GYRATION
> cv_ni = 6405, cv_nr = 1
> cv_i = (973:7377)
> cv_r = (21.5)
> /
>
> I saw the short discussion on this topic in the archive but there was no
> resolution of how to do it.
>
> Of course if anybody has an idea how to optimize the micelle without the
> RofG constraint that would also be appreciated.
> Thanks for your help,
>
> Roman Osman
> Department of Structural and Chemical Biology
> Mount Sinai School of Medicine
> New York, NY 10029
> Tel: 212-659-8627
> Fax: 212-849-2456
> e-mail: roman.osman.mssm.edu<mailto:roman.osman.mssm.edu><mailto:rom
> an.osman.mssm.edu>
>
>
>
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>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu<mailto:roitberg.ufl.edu>
> 352-392-6972
>
>
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>
> Roman Osman
> Department of Structural and Chemical Biology
> Mount Sinai School of Medicine
> New York, NY 10029
> Tel: 212-659-8627
> Fax: 212-849-2456
> e-mail: roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
>
>
>
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>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Wed Feb 15 2017 - 14:00:02 PST
