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
>>>>>
>>>>
>>>>
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Received on Fri Sep 01 2017 - 17:30:04 PDT
