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/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/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?
>> >>>>> _______________________________________________
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>> >>>>> 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 - 18:30:04 PDT
