[gmx-users] possible bug in convert-tpr

Mon Oct 16 14:42:54 CEST 2017

Hi All,
I think that there is a bug in "gmx convert-tpr", as I understand that 
"gmx dump" dumps wrong atom types and some wrong numbers when working 
with some modified tpr files. I attach clear instructions on how to get 
the bug, as well as two input files and the faulty .trp.

I found the problem using VOTCA's command csg_dump, and reported it to them:
    https://groups.google.com/forum/#!topic/votca/ogRTNFRL4RA
but after some discussion they said I should report it to you.

Could you please have a look at this? Please have a read at the 
discussion in VOTCA's email list to make sense of it all.

Many thanks,
Albert

P. S. - I just attached the most basic files to reproduce the bug. I 
could attach more, but that would exceed the 50K limit that the list 
imposes. In any case, the rest of the files can be found in the VOTCA 
email thread, previously commented.

-- 
---------------------------------
    Dr Albert Solernou
    EPSRC Research Fellow,
    Department of Physics and Astronomy,
    University of Leeds
    Tel: +44 (0)1133 431451

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A 32 GLN
A 35 VAL
A 36 VAL
A 37 PHE
A 38 GLN
A 39 ASN
A 40 ARG
A 41 GLU
A 43 VAL
A 54 GLU
A 64 THR
A 65 ARG
A 66 GLY
A 67 THR
A 69 ARG
A 84 ASP
A 85 HIS
A 86 TYR
A 87 ALA
B 17 HIS
B 29 TYR
B 30 TYR
B 31 GLY
B 33 ASN
B 34 LEU
B 35 ASP
B 36 ALA
B 38 TRP
B 39 ASP
B 40 CYS
B 42 THR
B 43 GLY
B 44 TRP
B 73 VAL
B 76 GLU
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[ Interface ]
 432  433  434  435  436  437  438  439  440  441  442  443  444  445  446 
 447  448  468  469  470  471  472  473  474  475  476  477  478  479  480 
 481  482  483  484  485  486  487  488  489  490  491  492  493  494  495 
 496  497  498  499  500  501  502  503  504  505  506  507  508  509  510 
 511  512  513  514  515  516  517  518  519  520  521  522  523  524  525 
 526  527  528  529  530  531  532  533  534  535  536  537  538  539  540 
 541  542  543  544  545  546  547  548  549  550  551  552  553  554  555 
 556  557  558  559  560  561  562  563  564  565  566  567  568  569  570 
 571  572  573  574  575  576  577  578  579  580  581  582  583  584  585 
 586  587  588  589  601  602  603  604  605  606  607  608  609  610  611 
 612  613  614  615  616  779  780  781  782  783  784  785  786  787  788 
 789  790  791  792  793  933  934  935  936  937  938  939  940  941  942 
 943  944  945  946  947  948  949  950  951  952  953  954  955  956  957 
 958  959  960  961  962  963  964  965  966  967  968  969  970  971  972 
 973  974  975  976  977  978  979  980  981  982  983  984  985  986  987 
 988  989  990  991 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 
1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1245 1246 
1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 
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1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 
1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1701 1702 
1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 
1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 
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1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 
1949 1950 1951 1952 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 
1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 
1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 
2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2042 
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2073 2074 2075 2076 2077 2078 2079 2080 2081 2082 2083 2084 2085 2086 2087 
2088 2108 2109 2110 2111 2112 2113 2114 2115 2116 2117 2118 2119 2120 2121 
2122 2123 2124 2125 2126 2127 2128 2129 2130 2131 2132 2133 2134 2135 2136 
2137 2138 2139 2140 2141 2142 2143 2144 2145 2146 2147 2148 2149 2150 2151 
2152 2612 2613 2614 2615 2616 2617 2618 2619 2620 2621 2622 2623 2624 2625 
2626 2627 2672 2673 2674 2675 2676 2677 2678 2679 2680 2681 2682 2683 2684 
2685 2686 
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# Gromacs - parse the PDB, define a box, solvate, neutralise with ions and minimise:
gmx pdb2gmx -f 1ay7.pdb -merge all -ignh -o gmx1ay7.pdb
gmx editconf -f gmx1ay7.pdb -o 1ay7.gro -d 1.0 -bt dodecahedron
gmx solvate -cp 1ay7.gro -cs spc216.gro -o 1ay7Solv.gro -p topol.top
gmx grompp -f ions.mdp -c 1ay7Solv.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -o 1ay7SolvIons.gro -p topol.top -pname NA -nname CL -np 13
gmx grompp -f minim-slow.mdp -c 1ay7SolvIons.gro -p topol.top -o em.tpr
mpirun  gmx_mpi mdrun -v -pin on -deffnm em

# Gromacs - start equilibration: a short trajectory at 100K, NVT:
gmx grompp -f nvt-100.mdp -c em.gro -p topol.top  -o nvt-100.tpr
mpirun  gmx_mpi mdrun -v -pin on -deffnm nvt-100

# interfaceResidues.txt is a list of residues at the interface of the complex
# selection.ndx contains the GMX atoms at the interface
# One can get the PDB of the interface to check that the numbers are fine:
gmx trjconv -f nvt-100.trr -s nvt-100.tpr -o nvt-100_interface.pdb -b 0 -e 0 -n selection.ndx

# Now set up 2 more tpr files, and one won't work in csg_dump:
gmx convert-tpr -s nvt-100.tpr -o nvt-100_protein.tpr < protein
gmx convert-tpr -s nvt-100.tpr -o nvt-100_interface.tpr -n selection.ndx 

csg_dump --top nvt-100.tpr | grep -v SOL | grep -v 'Resname NA' | grep -v 'Resname CL' > csgDump_system
csg_dump --top  nvt-100_protein.tpr | grep -v SOL | grep -v 'Resname NA' | grep -v 'Resname CL' > csgDump_protein
csg_dump --top  nvt-100_interface.tpr | grep -v SOL | grep -v 'Resname NA' | grep -v 'Resname CL' > csgDump_interface
# and csgDump_interface is wrong. 