> desc MEM.CHIE
On 9/3/17 6:12 PM, Parviz Seifpanahi Shabane wrote:
> UNIT name: default_name
> Head atom: null
> Tail atom: null
> Contents:
> R<CHIE 97>
>
> On Sun, Sep 3, 2017 at 9:11 PM, Bill Ross <ross.cgl.ucsf.edu
> <mailto:ross.cgl.ucsf.edu>> wrote:
>
> > desc MEM
>
> to see what is in it.
>
> Bill
>
>
> On 9/3/17 6:10 PM, Parviz Seifpanahi Shabane wrote:
>> 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
>> <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
>> <mailto: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
>> <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 <mailto: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 <mailto: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
>> <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?
>> >>>>> _______________________________________________
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>> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
>> <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
>
>
>
>
> --
> Parviz Seifpanahi
> Ph.D. Candidate
> Department of Physics
> Virgina Tech, Blacksburg, Va 24061
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Received on Sun Sep 03 2017 - 18:30:05 PDT
