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 - 14:30:02 PDT
