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?
>>>> _______________________________________________
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>>>>
>>>
>>>
>>>
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Received on Fri Sep 01 2017 - 17:30:03 PDT
