Date: Wed, 6 Apr 2022 15:43:46 +0000 (UTC)
Hi Dr. Horn,
Thank you for your kind reply. I have solved the format issue. Right now, I am facing a different problem. The O3B and O3A atoms are too close in the terminal phosphate region. I have attached the snapshot of the GDP. The following details of leap file are:
source leaprc.protein.ff14SBaddAtomTypes {{ "O" "O" "sp2" } { "O3" "O" "sp2" } { "O2" "O" "sp2" } { "OW" "O" "sp3" }}
loadamberprep gdp.prepcloadamberparams gdp.frcmodsavepdb GDP gdp.pdbm = loadpdb gdp.pdbsaveamberparm m gdp.prmtop gdp.inpcrdquit
Thanks and Regards,
Saikat Pal
On Wednesday, 6 April, 2022, 09:22:00 am GMT-4, Dr. Anselm Horn <anselm.horn.fau.de> wrote:
Saikat,
maybe you could provide some more details about your problem, i.e. the
complete leap input file.
Did you use the entry "GDP (revised phosphate parameters)" from Carlson?
Did you change something in the downloaded files?
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 05.04.2022 um 19:07 schrieb Saikat Pal:
> Dear all,
> I am trying to use GDP parameter of bryce group (AMBER parameter database (Bryce Group: Computational Biophysics and Drug Design - University of Manchester)
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> AMBER parameter database (Bryce Group: Computational Biophysics and Drug...
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> However, It shows the following error:
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> tleap -s -f rgs_tleap.in -I: Adding /home/saikat/softwares/amber20/dat/leap/prep to search path.-I: Adding /home/saikat/softwares/amber20/dat/leap/lib to search path.-I: Adding /home/saikat/softwares/amber20/dat/leap/parm to search path.-I: Adding /home/saikat/softwares/amber20/dat/leap/cmd to search path.-s: Ignoring all leaprc startup files.-f: Source rgs_tleap.in.
> Welcome to LEaP!Sourcing: ./rgs_tleap.inLoading Prep file: ./gdp.prepc
> /home/saikat/softwares/amber20/bin/teLeap: Error!residue CT 12.01 atom 16.00: name must be <= 4 charactersLoading parameters: ./gdp.frcmodReading force field modification type file (frcmod)Reading title: 0 0 2
> /home/saikat/softwares/amber20/bin/teLeap: Warning!Unknown keyword (R-GUANOSINE - with terminal diphosphate ) in parameter file. Perhaps a format issue?
> /home/saikat/softwares/amber20/bin/teLeap: Warning!Unknown keyword (gdp.db94) in parameter file. Perhaps a format issue?
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> Thanks and Regards,
> Saikat Pal
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(image/png attachment: gdp.png)
