[gmx-users] (no subject)
Kingsley Theras Primus Dass .
105726107 at gms.tcu.edu.tw
Tue Nov 8 12:13:46 CET 2016
Even when I add the new atom types to aminoacid.rtp, .hdb , .atp ,
Still it shows the same error ....
Could you please suggest some solutions.
Thank you in advance
On 8 Nov 2016 6:59 p.m., "Justin Lemkul" <jalemkul at vt.edu> wrote:
> On 11/7/16 10:44 PM, Kingsley Theras Primus Dass . wrote:
>> Hello users!!
>> I generated a Topology file for SO3- using ATB topology generator , which
>> is compatible with GROMACS. Then I copied the .rtp file from ATB and
>> it into GROMACS aminoacid.rtp.
>> The partial charge of aminoacid sulfated-tyrosine was -1.
>> When I run -pdb2gmx there was error saying the atoms were missing ,
>> Program gmx pdb2gmx, VERSION 5.1
>> Source code file:
>> line: 1584
>> Fatal error:
>> There were 6 missing atoms in molecule Protein_chain_D, if you want to use
>> this incomplete topology anyhow, use the option -missing
>> then I ran pdb2gmx -ignh -p topol.top -missing
>> It generated the topology file. But the parital charge of sulfated
>> was changed to -2, coz of missing hydrogen atoms.
>> can you please suggest some solutions , to overcome this problem.
> Add an .hdb entry for your residue so that pdb2gmx will build the missing
> atoms. In general, never use the -missing option.
> 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
> 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.
More information about the gromacs.org_gmx-users