If they aren't bonded to other atoms, yes.
Bill
On 8/19/16 6:28 PM, Neha Gandhi wrote:
> Does that mean I m better off defining phosphate, calcium and OH as
> individual residues?
>
> On 20 Aug 2016 7:06 AM, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
>
>> Looking at ambpdb's rendition of Neha's inpcrd, prmtop, to my mind there
>> should not be TER cards within a residue. The basic problem might be
>> trying to express everything as one residue. I'm not up-to-date enough
>> to guess exactly why ambpdb is putting TERs in there, but it seems like
>> a problem to me. Two snippets below to illustrate.
>>
>> Bill
>>
>> CRYST1 43.924 52.874 40.136 90.00 90.00 90.00 1
>> ATOM 1 O11 HAP 1 17.911 21.033 17.113 1.00
>> 0.00 O
>> ATOM 2 O12 HAP 1 17.911 21.033 19.584 1.00
>> 0.00 O
>> ATOM 3 P1 HAP 1 18.693 21.483 18.349 1.00
>> 0.00 P
>> ATOM 4 O13 HAP 1 18.713 23.020 18.349 1.00
>> 0.00 O
>> ATOM 5 O14 HAP 1 20.118 20.914 18.349 1.00
>> 0.00 O
>> TER 6 HAP 1
>> ATOM 6 O21 HAP 1 18.975 25.690 17.113 1.00
>> 0.00 O
>> ATOM 7 O22 HAP 1 18.975 25.690 19.584 1.00
>> 0.00 O
>> ATOM 8 P2 HAP 1 18.195 26.142 18.349 1.00
>> 0.00 P
>> ATOM 9 O23 HAP 1 16.854 25.391 18.349 1.00
>> 0.00 O
>> ATOM 10 O24 HAP 1 17.975 27.660 18.349 1.00
>> 0.00 O
>>
>> And later:
>>
>> ATOM 39 CA19 HAP 1 18.293 20.193 21.786 1.00
>> 0.00 CA
>> TER 40 HAP 1
>> ATOM 40 CA20 HAP 1 24.220 18.286 21.786 1.00
>> 0.00 CA
>> TER 41 HAP 1
>> ATOM 41 O1 HAP 1 17.099 18.232 22.144 1.00
>> 0.00 O
>> ATOM 42 H1 HAP 1 17.099 18.232 23.254 1.00
>> 0.00 H
>> TER 43 HAP 1
>> ATOM 43 O71 HAP 1 22.620 29.189 17.113 1.00
>> 0.00 O
>> ATOM 44 O72 HAP 1 22.620 29.189 19.584 1.00
>> 0.00 O
>> ATOM 45 P7 HAP 1 23.402 29.639 18.349 1.00
>> 0.00 P
>>
>>
>>
>> On 8/19/16 1:57 AM, Neha Gandhi wrote:
>>> I am adding further details (see the trail of emails below)
>>>
>>> Instead of minimizing supercell, I tried to look at unit cell and check
>> the
>>> minimzation.
>>>
>>> The unit cell dimensions are correct (I checked in vmd, materials studio,
>>> and also tried setBox m1 centers/vdw)
>>> I also tried increasing the box size in each dimension by 1 A.
>>>
>>> As Bill suggested, I tried visualising the trajectory of initial
>> structure
>>> versus minimzation rst file. It seems although I am holding the HAP atoms
>>> fixed (ntr=1, restraint weight >> 500) in the cell, the atoms are moving
>>> and affects the geometry.
>>>
>>> .Bill: I also tried fixatomorder in case the inpcrd has some issues, but
>> it
>>> didn't make any difference to my results. When I output the min.rst as
>> pdb,
>>> it has correct elements in the last column.
>>>
>>> How do I work around this problem? How to fix HAP surface?
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 18 August 2016 at 23:13, David A Case <david.case.rutgers.edu> wrote:
>>>
>>>> On Thu, Aug 18, 2016, Neha Gandhi wrote:
>>>>> I have a pdb file of a unit cell and I am converting using antechamber
>> to
>>>>> mol2 file
>>>> It sounds like the problem might be right here: how did you get this
>> file?
>>>> Are you sure that the unit cell parameters (in the CRYST1 line) are
>>>> correct?
>>>>
>>>>> I prepare supercell from the input file which has unit cell information
>>>>> PropPDB -p input.pdb -o supercell.pdb -ix 15 -iy 9 -iz 4
>>>>>
>>>>>>> $AMBERHOME/bin/tleap -s -f leaprc.ff99SBildn
>>>>>> source leaprc.hap
>>>>>> loadamberparams frcmod.hap
>>>>>> loadoff hap.lib
>>>>>> m1=loadpdb supercell.pdb
>>>>>> set m1 box {145 150 39}
>>>> The "supercell.pdb" file should already
>>>> have the proper Unit Cell values. Are they different than {145 150 39}?
>>>>> cpptraj -p supercell.prmtop -i ptraj.in
>>>>> ---
>>>>> trajin correct.inpcrd
>>>>> check reportfile report.dat
>>>>>
>>>>> The report.dat file is empty so I assume there are no overlaps.
>>>> I agree that this is very odd, given the huge vdW energy on the first
>> step
>>>> of minimization.
>>>>
>>>>> I try to run minimization using pmemd.MPI and that's where I am not
>> able
>>>> to
>>>>> figure out why the structure shows high energies and min.rst file
>> doesn't
>>>>> look right. I convert min.rst file using cpptraj to pdb. It seems that
>>>>> calcium ion (NG) is interpreted as carbon or some other atoms ...
>>>> Can you say what it is about the PDB file that led you the think that
>> the
>>>> calcium ion is interpreted as carbon? PDB files have the element at the
>>>> far
>>>> right of the ATOM card...what does that show?
>>>>
>>>> ....dac
>>>>
>>>>
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>>>
>>
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Received on Fri Aug 19 2016 - 19:00:03 PDT
