[gmx-users] Atomtype P,SI not found from grompp
quyviolet at gmail.com
Fri Jan 23 17:51:05 CET 2015
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
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?
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
>> 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 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
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