Feng,
Thanks very much; I’ll try it out.
Rami
On Feb 15, 2017, at 4:56 PM, Feng Pan <fpan3.ncsu.edu<mailto:fpan3.ncsu.edu>> wrote:
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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pfreezer_AmberPatch&d=DwICAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=q8vs_fbTOEJjOKNIgjun94sbqYxVkxfOTdUE1xTyUk0&m=P4TXVw4OkCwlyeDONeLfGt249DMM3sg_JsJ6c1jEglQ&s=YvL0wUODKEBFBMknoUUjLXateBWu8XI3oZwqMlQYQPo&e=
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<mailto: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><mailto:
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:roman.osman.mssm.edu><mailto:rom> an.osman.mssm.edu<mailto:an.osman.mssm.edu>>
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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><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<mailto:fpan3.ncsu.edu>
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Roman Osman
Professor of Structural and Chemical Biology
Mount Sinai School of Medicine
New York, NY 10029
(212) 659-8627
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Received on Wed Feb 15 2017 - 17:00:03 PST
