[gmx-users] Atomtype P,SI not found from grompp

[Jennifer Vo]

Dear Justin,
Now I get it. Thanks a lot for taking your time. I sent the email to the
author of ATB developer and still waiting for the answer.
Many thanks again.
Regards,
Jennifer

On Fri, Jan 23, 2015 at 5:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/23/15 11:51 AM, Jennifer Vo wrote:
>
>> Dear Justin,
>> Thanks a lot. I tried to use all of the NADPH from ATB (
>> http://compbio.biosci.uq.edu.au/atb/index.py) and they have the same
>> problem.
>> Regarding the "P, SI", ist atom type "P, SI" (with one space in between)
>> is
>> existed in the gromos 54A7 force field
>> #define ga_26       120.00      530.00
>> ; P, SI  -  OA  -  CHn, P       95
>>
>> in file gromos54a7.ff/ffbonded.itp. It means it's not a new atom type, did
>> I interpret correctly?
>>
>>
> No.  The comment does not tell you that "P,SI" is an atom type.  It tells
> you that the angle parameter there is applicable to either P or SI in the
> first position (atom i), OA in the second position (atom j), then either
> CHn or P in the last position (atom k).  The available atom types for the
> force field are in atomtypes.atp.  If it's not there, it's not real.  I
> recall our previous discussions about the source of the topology.
> Hopefully you have alerted the ATB developers to the erroneous topology
> that they're distributing.
>
> If your atom is a phosphorus, the atom type is P.  Don't change it.  If
> the parameters are sub-par, then derive new ones or choose a better force
> field.
>
> -Justin
>
>
>  Regards,
>> Jennifer
>>
>> On Fri, Jan 23, 2015 at 5:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 1/23/15 9:52 AM, Jennifer Vo wrote:
>>>
>>>  Dear Justin,
>>>> I did try replacing the "P,SI" to "P"  but the ligand was distorted
>>>> during
>>>> energy minimization (error happened excactly at the position of P).
>>>> Then I
>>>> tried replacing "P,SI" to "P, SI" (with one space in between)  according
>>>> to
>>>> the existed gromos54a7 force field but got the error when running
>>>> grompp:
>>>> *Too few parameters on line (62) *
>>>>
>>>> which is the line of "3 P, SI" as following:
>>>>
>>>> ;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
>>>>       1    OA    1    NAP     O1X    1   -0.797 15.9994
>>>>       2     H    1    NAP      H4    1    0.295   1.0080      ; -0.502
>>>>       3 P, SI    1    NAP     P2B    2    2.585  30.9738
>>>>       4    OM    1    NAP     O3X    2   -1.083  15.9994
>>>>       5    OA    1    NAP     O2X    2   -0.797 15.9994
>>>> Keep playing around by replacing "P, SI" with "PSI" on all files but it
>>>> also didn't work,
>>>> Could you please help me for a solution in this case?
>>>>
>>>>
>>> If the parameters provided distort the structure, you need to find or
>>> derive better ones.  You can't sub in nonsensical atom types and hope for
>>> it to work :)
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>