Hi Thomas,
Thanks for your reply!
Yes, I tried using igb=0, and the simulation just stopped at reading
restart file. The error message gives a segmentation fault so I think there
might be something wrong with the input file I'm using.
Actually, I'm trying to calculate the relative binding free energy of a
peptide mutation involving charge-changing (e.g. mutating Asp to Ala, with
the charge changing from -1 to 0). So far I've tried using co-alchemical
ions to balance the charge between the two systems, or running the
simulation without any correction of the changed charge. Both failed.
So I'm thinking if I could firstly calculate the energy change of mutation
on gas phase, and secondly calculate the solvation energy difference of the
wild-type and mutant, and then sum the two terms up.
I cannot figure out any other methods in TI to calculate the mutation
involving charge-changing :(. It would be appreciated if you could give me
any suggestions on this.
Best,
Fanyu
On Mon, Jun 5, 2023 at 3:29 PM Steinbrecher, Thomas <
thomas.steinbrecher.roche.com> wrote:
> Hi Fanyu,
>
> have you tried running with igb = 0 ? It should be the same effect as
> igb=6 based on what I see in the manual, but maybe there is a check in
> pmemd about "igb > 0" that is missing that igb = 6 would also correspond to
> vacuum?
>
> As a side note, based on the masks, you seem to have a 10+ residue peptide
> in your simulation, are you sure a vacuum simulation of this species is
> meaningful?
>
> Kind Regards,
>
> Thomas
>
> On Mon, Jun 5, 2023 at 4:26 AM Fanyu Zhao via AMBER <amber.ambermd.org>
> wrote:
>
>> Dear amber users,
>>
>> I'm trying to run TI in the gas phase. But it always gives me an error
>> message of "The CUDA code currently cannot handle TI with implicit solvent
>> models! Please use the serial code instead".
>>
>> I was wondering if gas phase TI can only be performed with CPU and if I'm
>> correct with the process of creating a pdb file in gas phase.
>>
>> Here's my input for a minimization.
>>
>> Minimization with position restraint
>> &cntrl
>> imin = 1, ntmin = 2, maxcyc = 10000,
>> ntpr = 1000, ntwe = 1000,
>> ntr = 1, restraint_wt = 100.0,
>> restraintmask = '!.H= ',
>> ntb=0,igb=6, cut = 9999.0, ioutfm = 1,
>> icfe = 1, ifsc = 1, logdvdl = 0,
>> timask1=':10',
>> timask2=':3',
>> scmask1=':10 & !.CA,C,N,O',
>> scmask2=':3 & !.CA,C,N,O',
>> clambda=0.5,
>> &end
>> /
>>
>>
>> And here's the tleap file I used to generate a gas phase pdb file.
>>
>> source leaprc.protein.ff14SB
>>
>> com=loadpdb 1tvb_aftermd.pdb
>> unbound=loadpdb peptide.pdb
>>
>> savepdb com wild_md_bound.pdb
>> saveamberparm com wild_md_bound.prmtop wild_md_bound.inpcrd
>>
>> savepdb unbound wild_md_unbound.pdb
>> saveamberparm unbound wild_md_unbound.prmtop wild_md_unbound.inpcrd
>> quit
>>
>>
>> Thank you so much!
>>
>> Best,
>> Fanyu
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=TA6Yv1GqGslhLaifgggoUQ&m=4WjHVK2ypm7vH0Okye8p2Ny0JAsKRcIz9NXV9bVSYGgs24GTPqJvmd0_PYIvgSFY&s=jj3P4Wq5mxqWq6hYdbE91qLTi7Stm6DKikZPbRtmspw&e=>
>>
>
>
> --
> *Dr. Thomas Steinbrecher*
> Principal Scientist CADD
>
> Roche Pharma Research and Early Development
> Roche Innovation Center Basel
> F. Hoffmann-La Roche Ltd
> Bldg. 092/3.92
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
>
> Phone +41 61 682 1319
> mailto: thomas.steinbrecher.roche.com
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 05 2023 - 01:00:02 PDT
