Dear All,
I could now figure out how to do this using explicit solvent:
important points to note:
1) while saving the topology files, *saveAmberParm* should be mentioned instead of *saveamberparm*, otherwise the topology files will not generated with leaprc.constph.
2) running : cpinutil.py -p *.parm7 -igb 2 -o *.cpin -op *.modO.parm7 -resnames AS4 GL4 HIP CYS
will give the below mentioned error:
Traceback (most recent call last):
File "/opt/amber16/bin/cpinutil.py", line 294, in <module>
main(opt)
File "/opt/amber16/bin/cpinutil.py", line 264, in main
parm.writeParm(opt.outparm)
AttributeError: 'AmberParm' object has no attribute 'writeParm'
Therefore, writeParm (on line 264) in $AMBERHOME/bin/cpinutil.pyshould be changed to write_parm, then it works fine.
thanks
Regards
Sowmya
________________________________________
From: Andreas Tosstorff [andreas.tosstorff.cup.uni-muenchen.de]
Sent: Tuesday, December 13, 2016 4:28 PM
To: AMBER Mailing List
Subject: Re: [AMBER] pka of CYS
What does your outputfile read?
On 12/13/2016 04:21 PM, Sowmya Indrakumar wrote:
> Dear All,
> Thank you for your suggestions.
>
> I included CYS in the list of -resnames and could create the *.cpin. I could run the minimisation properly using sander, but running heating step using pmemd.cuda gave this error message *STOP PMEMD Terminated Abnormally!*
> The above MD is been run for implicit solvent, but this doesn seem to work if I use explicit solvent (i get the same error message).
> Kindly, suggest me.
>
> Thanks
> Regards
> Sowmya
> ________________________________________
> From: Adrian Roitberg [roitberg.ufl.edu]
> Sent: Tuesday, December 13, 2016 3:18 PM
> To: amber.ambermd.org
> Subject: Re: [AMBER] pka of CYS
>
> Hi
>
> Have you tried just using CYS as a titratable residue ?
>
> If you try
>
> cpinutil.py -l
>
> you will see that CYS is already properly defined as titratable, with
> all parameters already there.
>
> You can also look at http://pubs.acs.org/doi/full/10.1021/ct401042b
>
> This is a paper by Jason Swails and myself, were there are some
> calculations for Cysteine.
>
> adrian
>
>
>
>
> On 12/13/16 8:43 AM, Eric Lang wrote:
>> Hi Carlos,
>> I think that as long as Cys is defined as being a titrable residue, the
>> partial charge on each atom of the residue for the two states (protonated
>> and deprotonated) are defined in titratable_residues.py (which is part of
>> Parmed). In particular the charge on the titrable hydrogen becomes 0.00 in
>> the deprotonated form and the charges on all atoms of the side chains are
>> changed to reflect the deprotonation. Overall during CpHMD the hydrogen are
>> not actually removed (i.e. changing from one residue type to another e.g.
>> CYS to CYM) but instead the hydrogen in "masked" by zeroing its charged and
>> changing the charge of adjacent atoms. It is a change of state (state 1 to
>> state 0 for the deprotonation of Cys) for a single residue type (CYS)
>> I believe however that the the Van der Waals radius does not change between
>> the protonated and deprotonated form as it does not seem to have an impact
>> on the quality of the result (as shown in the original Mongan paper where
>> the effect of the VdW radius of the titrable hydrogens in Lys (non-zero)
>> was compared with the radius of titrable hydrogens in Glu and Asp (where is
>> is zero)).
>> Please Jason, correct me if what I said is wrong or incomplete.
>> Eric
>>
>> On 13 December 2016 at 11:09, Carlos Simmerling <carlos.simmerling.gmail.com
>>> wrote:
>>> I don't think that will work. The parameters for Cys without the bond are
>>> not at all the same as a deprotonated (negatively charged) Cys. You will
>>> need to find or make Cys- parameters, and then develop the reference
>>> energies needed for the pka calculations. Someone else may have better info
>>> (Jason?).
>>>
>>> On Dec 13, 2016 2:33 AM, "Eric Lang" <eric.lang.bristol.ac.uk> wrote:
>>>
>>> Hi,
>>> You just need to add CYS to the list of titrable residues (using the
>>> resname flag for example) when you generate your cpin file with cpinutil.
>>> Eric
>>>
>>>
>>> On 12/12/2016 20:16, "Sowmya Indrakumar" <soemya.kemi.dtu.dk> wrote:
>>>
>>> Dear All,
>>> I am trying to calculate pka of CYS in a given protein at constph. I simply
>>> keep the bonded CYX-CYX as non-bonded CYS-CYS and remove the conect record
>>> from the PDB file before making the *.parm7 and *.rst7 files for MD.
>>>
>>> I am following whats mentioned in the given link to calculate the Pka of
>>> ASP,GLU and HIS : http://ambermd.org/tutorials/a
>>> dvanced/tutorial18/section1.
>>> htm <http://ambermd.org/tutorials/advanced/tutorial18/section1.htm> at
>>> constph.
>>>
>>> I did not come across any article which shows how to calculate pKa for CYS
>>> residues. Kindly, suggest me on this.
>>>
>>> Thanks
>>> Sowmya
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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>
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--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Tue Dec 13 2016 - 08:30:03 PST
