[gmx-users] converting .gro trajectory to .pdb

Wed Jan 18 18:47:10 CET 2017

It still asks for a .tpr file, though:

Command line:
  gmx trjconv -f conf_complete.gro -o file.pdb

Will write pdb: Protein data bank file

-------------------------------------------------------
Program gmx trjconv, VERSION 5.1.2
Source code file: /Users/irem/Downloads/gromacs-5.1.2/src/gromacs/fileio/gmxfio.c, line: 476

Can not open file:
topol.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Best,
Irem

> On Jan 18, 2017, at 6:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 1/18/17 12:32 PM, Irem Altan wrote:
>> Hi,
>> 
>> It gives me an error saying
>> 
>> Fatal error:
>> Index[1556] 3148 is larger than the number of atoms in the
>> trajectory file (3145). There is a mismatch in the contents
>> of your -f, -s and/or -n files.
>> 
>> I’m guessing this is because I had created the original .gro file by just using the protein heavy atoms, but the .tpr file obviously has the indices according to the entire system.
>> 
> 
> You don't need to do anything as complex as what Dawid suggested.  You just need to convert the format:
> 
> gmx trjconv -f file.gro -o file.pdb
> 
> -Justin
> 
>> Best,
>> Irem
>> 
>> On Jan 18, 2017, at 4:22 PM, Dawid das <addiw7 at googlemail.com<mailto:addiw7 at googlemail.com>> wrote:
>> 
>> Hi,
>> 
>> I guess you can try
>> gmx trjconv -f  file.gro -o file.pdb -pbc mol -s file.tpr -center
>> 
>> 2017-01-18 16:14 GMT+01:00 Irem Altan <irem.altan at duke.edu<mailto:irem.altan at duke.edu>>:
>> 
>> Hi,
>> 
>> I have a trajectory saved in .gro format. It has multiple frames/snapshots
>> in it. I’m using .gro format because I needed higher precision than
>> standard .pdb precision, but now I can’t visualize it with VMD. I would
>> like to convert this to .pdb, and I tried editconf to do this. The problem
>> is, it only converts the first frame. How can I convert the entire
>> trajectory from .gro to .pdb?
>> 
>> Best,
>> Irem
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ut9Eg1mdv7zQ87J-Hr4jmzt8kZPErp4ReBZA3Y1R4IU&s=_Mbq7Ee36TSIeJmtww8KtPHkcnAjzNFasyibW8h-xUI&e=
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> 
>> * Can't post? Read https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ut9Eg1mdv7zQ87J-Hr4jmzt8kZPErp4ReBZA3Y1R4IU&s=Cn8HcZZss9LwftQ8X1PiU081ohM_xzp-46vFnWCuPDE&e=
>> 
>> * For (un)subscribe requests visit
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ut9Eg1mdv7zQ87J-Hr4jmzt8kZPErp4ReBZA3Y1R4IU&s=zTTGwLxX0aqF2aSAMz8Z2wiynKR8cw-otOWjcFnqSus&e=  or
>> send a mail to gmx-users-request at gromacs.org<mailto:gmx-users-request at gromacs.org>.
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists_GMX-2DUsers-5FList&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ut9Eg1mdv7zQ87J-Hr4jmzt8kZPErp4ReBZA3Y1R4IU&s=AYYJWJRv7EoUR_y7lDcAA9ce-Zsfo1YRqd2Wpgsk6DI&e=  before posting!
>> 
>> * Can't post? Read https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ut9Eg1mdv7zQ87J-Hr4jmzt8kZPErp4ReBZA3Y1R4IU&s=Cn8HcZZss9LwftQ8X1PiU081ohM_xzp-46vFnWCuPDE&e=
>> 
>> * For (un)subscribe requests visit
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ut9Eg1mdv7zQ87J-Hr4jmzt8kZPErp4ReBZA3Y1R4IU&s=zTTGwLxX0aqF2aSAMz8Z2wiynKR8cw-otOWjcFnqSus&e=  or send a mail to gmx-users-request at gromacs.org<mailto: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
> https://urldefense.proofpoint.com/v2/url?u=http-3A__mackerell.umaryland.edu_-7Ejalemkul&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ai8ElDCY2hiNVXG1jgfq2LtVT47H2dRnB0jaxQEb2UE&s=AIdpNPJpEwE6a5lNAyxc7z2HWyXEDC-VWMB_hPBdfes&e= 
> ==================================================
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists_GMX-2DUsers-5FList&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ai8ElDCY2hiNVXG1jgfq2LtVT47H2dRnB0jaxQEb2UE&s=ReE9ET9FoSs68DXsJvEus1wbH8mqTZP05380kMXdECo&e=  before posting!
> 
> * Can't post? Read https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ai8ElDCY2hiNVXG1jgfq2LtVT47H2dRnB0jaxQEb2UE&s=jpXnx76EN85zj3ISUkcIytc07OV16bnQH3CKQsAd55c&e= 
> * For (un)subscribe requests visit
> https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=ai8ElDCY2hiNVXG1jgfq2LtVT47H2dRnB0jaxQEb2UE&s=lfmA9BkKh3z6A8qKz6BAJiMree4bJxKpygYy1vSB8yY&e=  or send a mail to gmx-users-request at gromacs.org.