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
> <mailto: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
>> <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?
>>> >>>>> _______________________________________________
>>> >>>>> AMBER mailing list
>>> >>>>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>>> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> <http://lists.ambermd.org/mailman/listinfo/amber>
>>> >>>>>
>>> >>>>
>>> >>>>
>>> >>>> _______________________________________________
>>> >>>> AMBER mailing list
>>> >>>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>>> >>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> <http://lists.ambermd.org/mailman/listinfo/amber>
>>> >>> _______________________________________________
>>> >>> AMBER mailing list
>>> >>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>>> >>> http://lists.ambermd.org/mailman/listinfo/amber
>>> <http://lists.ambermd.org/mailman/listinfo/amber>
>>> >>>
>>> >>
>>> >
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> <http://lists.ambermd.org/mailman/listinfo/amber>
>>> >
>>>
>>>
>>> _______________________________________________
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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
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Received on Sun Sep 03 2017 - 18:30:06 PDT
