Got it Thank you.
set HIC head MEM.CHIE.N
On Sun, Sep 3, 2017 at 9:17 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Now you should be able to infer how to reference atoms in the residue when
> setting head and tail.
>
> On 9/3/17 6:15 PM, Parviz Seifpanahi Shabane wrote:
>
> RESIDUE name: CHIE
> RESIDUE sequence number: 97
> RESIDUE PDB sequence number: 1
> Type: protein
> Connection atoms:
> Connect atom 0: A<N 1>
> Improper torsions:
> Contents:
> A<OXT 18>
> A<O 17>
> A<C 16>
> A<HD2 15>
> A<CD2 14>
> A<HE2 13>
> A<NE2 12>
> A<HE1 11>
> A<CE1 10>
> A<ND1 9>
> A<CG 8>
> A<HB3 7>
> A<HB2 6>
> A<CB 5>
> A<HA 4>
> A<CA 3>
> A<H 2>
> A<N 1>
> A<CU 19>
>
> On Sun, Sep 3, 2017 at 9:14 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> > 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> 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/sc
>>> ript1.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/a
>>>> dvanced/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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>>>> >>> _______________________________________________
>>>> >>> AMBER mailing list
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>>>> >>>
>>>> >>
>>>> >
>>>> > _______________________________________________
>>>> > AMBER mailing list
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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
>>
>>
>>
>
>
> --
> 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 - 18:30:07 PDT
