Thank you, Bill. right now everything works except setting the tail and
head of the residue. first I used this commands from the tutorial which
are not correct
set MEM head MEM.MEM.N
set MEM tail MEM.MEM.C
and then I tried something like this
set MEM head MEM.1.N
from here (
http://upjv.q4md-forcefieldtools.org/REDDB/projects/F-86/script1.ff).
and I got this error:
The value must be of the type: Atom
?
On Fri, Sep 1, 2017 at 8:03 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Oops, or change CU to Cu in the NONBON of your frcmod.
>
> Bill
>
>
> On 9/1/17 5:01 PM, Bill Ross wrote:
> > E.g. you have
> >
> > mods = loadAmberParams frcmod.ionsjc_tip3p
> >
> > Look at that file, and emulate it for the params of your Cu.
> >
> > Bill
> >
> > On 9/1/17 4:57 PM, Parviz Seifpanahi Shabane wrote:
> >> I am using Amber 16 on Ubuntu 16.04, I followed your suggestions but got
> >> something (Could not see the N). I tried something new instead of using
> my
> >> PDB files, in xleap, I started from Thr residue, means
> >>> edit THR
> >> and then added the CU atoms to the structure and then
> >>> saveoff THR TCU.lib
> >> after that manually I changed all THR inside of this lib file to TCU. by
> >> this trick problem with the lib file solved (I do not get atom type
> error
> >> anymore).
> >> for TCU.frcmod (for CU ions) I used the file in the tutorial (
> >> http://ambermd.org/tutorials/advanced/tutorial1_adv/index.htm):
> >>
> >> # modifications to force field for poplar plastocyanin
> >>
> >> MASS
> >> SM 32.06
> >> CU 65.36
> >>
> >> BOND
> >> NB-CU 70.000 2.05000 #kludge by JRS
> >> CU-S 70.000 2.10000 #kludge by JRS
> >> CU-SM 70.000 2.90000 #for pcy
> >> CT-SM 222.000 1.81000 #met(aa)
> >>
> >> ANGLE
> >> CU-NB-CV 50.000 126.700 #JRS estimate
> >> CU-NB-CR 50.000 126.700 #JRS estimate
> >> CU-NB-CP 50.000 126.700 #JRS estimate
> >> CU-NB-CC 50.000 126.700 #JRS estimate
> >> CU-SM-CT 50.000 120.000 #JRS estimate
> >> CU-S -CT 50.000 120.000 #JRS estimate
> >> CU-S -C2 50.000 120.000 #JRS estimate
> >> CU-S -C3 50.000 120.000 #JRS estimate
> >> NB-CU-NB 10.000 110.000 #dac estimate
> >> NB-CU-SM 10.000 110.000 #dac estimate
> >> NB-CU-S 10.000 110.000 #dac estimate
> >> SM-CU-S 10.000 110.000 #dac estimate
> >> CU-SM-CT 50.000 120.000 #JRS estimate
> >> CT-CT-SM 50.000 114.700 #met(aa)
> >> HC-CT-SM 35.000 109.500
> >> H1-CT-SM 35.000 109.500
> >> CT-SM-CT 62.000 98.900 #MET(OL)
> >>
> >> DIHE
> >> X -NB-CU-X 1 0.000 180.000 3.000
> >> X -CU-SM-X 1 0.000 180.000 3.000
> >> X -CU-S -X 1 0.000 180.000 3.000
> >> X -CT-SM-X 3 1.000 0.000 3.000
> >>
> >> NONBON
> >> CU 2.20 0.200
> >> SM 2.00 0.200
> >>
> >> The new error that I am getting is
> >> For atom: .R<YCU 138>.A<Cu22 22> Could not find vdW (or other)
> >> parameters for type: Cu
> >> and this my leap script:
> >> source $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff10
> >> loadoff YCU1.lib
> >> loadamberparams YCU.frcmod
> >> loadAmberParams frcmod
> >> set default PBradii bondi
> >> mods = loadAmberParams frcmod.ionsjc_tip3p
> >> mol = loadpdb H4-DNA-Mutated-clean-YAG-test.pdb
> >>
> >> #addions mol Na+ 0
> >> #addions mol Cl- 0
> >>
> >> #addions2 mol Na+ 34
> >> #addions2 mol Cl- 34
> >>
> >> solvateBox mol OPCBOX 4.22 iso
> >> saveamberparm mol H4-DNA-OPC-FF10.top H4-DNA-OPC-FF10.crd
> >> quit
> >>
> >> What should I do now?
> >>
> >> Thank you for you help.
> >>
> >>
> >>
> >>
> >>
> >> On Thu, Aug 31, 2017 at 3:50 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >>
> >>> You should be able to click the draw box top right, then click on one
> >>> atom and draw to the next before releasing.
> >>>
> >>> If that doesn't work, what kind of hardware/OS are you running on?
> >>>
> >>> It would be faster to
> >>>
> >>> > x = loadpdb the.pdb
> >>>
> >>> > bondbydistance x
> >>>
> >>> > edit x
> >>>
> >>> Then delete the extra bonds, and draw the missing ones.
> >>>
> >>> Bill
> >>>
> >>>
> >>> On 8/31/17 10:11 AM, Parviz Seifpanahi Shabane wrote:
> >>>> Yes, I did, this what I am getting (attached image) after loading
> TMN.pdb
> >>>> to xleap.
> >>>>
> >>>> On Thu, Aug 31, 2017 at 1:02 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >>>>
> >>>>> I only see 1 N atom in the pdb below, and it appears in xleap.
> >>>>>
> >>>>> I was able to draw bonds between MN and O, N.
> >>>>>
> >>>>> Did you click on 'Draw' on the top of the xleap editor?
> >>>>>
> >>>>> Bill
> >>>>>
> >>>>> On 8/31/17 8:11 AM, Parviz Seifpanahi Shabane wrote:
> >>>>>> Dear AMBER users,
> >>>>>> I need to add the highly charged ion (-120 e) to my system in
> certain
> >>>>> place
> >>>>>> in my PDB file before running simulation, I am following this
> tutorial:
> >>>>>> http://ambermd.org/tutorials/advanced/tutorial1_adv/index.
> htm
> >>>>>> I picked the residue which has the best position (Threonine (Thr))
> for
> >>> my
> >>>>>> purpose and created the new residue named TMN by adding the Mn ion
> to
> >>> it.
> >>>>>> this my TMN.pdb file:
> >>>>>>
> >>>>>> ATOM 525 N TMN B 96 55.589 87.183 6.224 0.00 0.00
> >>>>> N
> >>>>>> ATOM 526 CA TMN B 96 56.332 86.013 5.728 0.00 0.00
> >>>>> C
> >>>>>> ATOM 527 C TMN B 96 57.725 86.436 5.230 0.00 0.00
> >>>>> C
> >>>>>> ATOM 528 O TMN B 96 57.865 87.357 4.412 0.00 0.00
> >>>>> O
> >>>>>> ATOM 529 CB TMN B 96 55.580 85.363 4.578 0.00 0.00
> >>>>> C
> >>>>>> ATOM 530 CG2 TMN B 96 56.358 84.123 3.985 0.00 0.00
> >>>>> C
> >>>>>> ATOM 531 OG1 TMN B 96 54.305 84.932 5.050 0.00 0.00
> >>>>> O
> >>>>>> ATOM 908 H TMN B 96 54.624 87.243 5.931 0.00 0.00
> >>>>> H
> >>>>>> ATOM 909 HA TMN B 96 56.448 85.287 6.533 0.00 0.00
> >>>>> H
> >>>>>> ATOM 910 HB TMN B 96 55.451 86.086 3.773 0.00 0.00
> >>>>> H
> >>>>>> ATOM 911 HG21 TMN B 96 55.745 83.227 4.084 0.00 0.00
> >>>>> H
> >>>>>> ATOM 912 HG22 TMN B 96 56.575 84.299 2.931 0.00 0.00
> >>>>> H
> >>>>>> ATOM 913 HG23 TMN B 96 57.292 83.985 4.530 0.00 0.00
> >>>>> H
> >>>>>> ATOM 914 HG1 TMN B 96 54.425 84.288 5.752 0.00 0.00
> >>>>> H
> >>>>>> ATOM 13626 MN TMN B 96 55.100 90.254 3.700 0.97 51.89
> >>>>> MN
> >>>>>> problem is in editing step for creating TMN unit and library file I
> can
> >>>>> not
> >>>>>> see the Nitrogen (N) atoms (edit TMN.pdb) and I can not draw the
> bonds
> >>>>>> correctly.
> >>>>>> any idea?
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
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> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >
> > _______________________________________________
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> >
>
>
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>
--
Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virgina Tech, Blacksburg, Va 24061
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Received on Sun Sep 03 2017 - 18:30:02 PDT
