Re: [AMBER] RST File Corrupt from Czarny,Ryan on 2020-04-14 (Amber Archive Apr 2020)

From: Czarny,Ryan <Ryan.Czarny.colostate.edu>
Date: Tue, 14 Apr 2020 19:05:26 +0000

Thanks Carlos, I added the ioutfm flag so I can get a text format.

Thanks!

Ryan S Czarny
BMB PhD Candidate - Ho Lab
Committee of University Programs - GSC Rep

________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Tuesday, April 14, 2020 12:03 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] RST File Corrupt

are you sure they are corrupt and not just using binary netcdf format?
we don't know which amber version or if you have set the ioutfm flag in
your mini.in file, but I suspect it is just binary format. Convert in
cpptraj, or perhaps set ioutfm if you really need text readable format.

On Tue, Apr 14, 2020 at 2:00 PM Czarny,Ryan <Ryan.Czarny.colostate.edu>
wrote:

> Hello Amber Community,
>
> I am running a minimization and have been getting corrupted .rst files
> that are causing errors with further calculations. I have tried multiple
> starting files and they all result in the same error.
>
> I am running Amber18 on a Mac running OS X El Cap 10.11.6.
>
> Below is my workflow:
>
> * Reduce pdb file
> * Run through tleap
> * Force field ff14SB.redq and parameter frcmod.ionsjc_tip3p
> * generate ion prmtop and inpcrd as well as water prmtop and inpcrd
> files
> * Start minimization
> * My all_min.mdinfo and all_min.out files look completely fine and
> exactly what I would expect but the .rst files look like the sample that I
> have provided below.
>
> Any assistance on this would be greatly appreciated.
>
>
> Thanks!
>
> ________________________________________________________________________
> CDF
> spatial atom SÅ cell_spatial label cell_angular title
> default_name application AMBER program pmemd programVersion 16.0
> Conventions AMBERRESTART ConventionVersion 1.0 time units
> picosecond Ù spatial ¸ coordinates units angstrom ‘
> cell_spatial ◊ cell_angular ◊ cell_lengths units angstrom
> ◊, cell_angles units degree ◊Dxyz.Sßu AE˘@RNY?Ò5@@O€ƒKÊ
> †@Sg1˛Qe’@RG »ÊÏ @O’Ô$œ Û@S∑ PÚ€u.RåV]»5…@O» j ˇ[@SºX‡,âü@R;£µ∑âv.P(#·∏
> .Sœ°] 3ñ@R †wò @OVö\Ï 2.T ßâv!/.R! F∫ ç@O^ıú˜ˇã@Sª … #Ã@Q∫zÌ
> áá.Or?πˆÃƒ.S”y– ı @Q•“¨[éΩ@OÓu~ ƒˇ@Su›·¡Ç @Q±G„$NO.Onﬂ”πh[@S·|˚ ]
> .Qâ-c¿É5.NÓŸ .”i.SªÄì¢àô@QY‰}⁄W°@N“X4]¥ @S≥$ ‘%Ù@R4yÜ ® @N§]q«éU.SfœßÁ5∆@RA)øÏÌÿ@NÜ
> Ÿ-q2.SÓÙf˛aÍ.R9)÷g±J.N)$/ )ì@T+ù¯Ûáâ@R': †k.NGQÌ6¢T.S›Û }˙…@ROÔ @¡j.MtVÉá
> ¨.S¬HÑ* ˛.Rê ùB +.Mo≤wŸƒ•@T4i…BH @RP¥^_'ê@M Ûpv.≠@T] ëGd/.RÅ Zsú
> .MNdÔ˚B9.TSéesÔF.R — ù{:.M%\ -yÎ.T0…ü$VÇ.Rb-+∆´Á@LR ¬, Â@Tr 7qc @Rc9≠˚†5.L
> ’‘“8 @T ŸÒ[·{.R. “ €ï@L ∆fÚ§@T ¨Ç„gÀ@R∑CyU3Œ@L% s i
> .SƒΩ ) Ï.R∂Vê\≈±.LWKŒ U.T(óB„“›@RÎô ;o.Laì‰Jdõ@T ¬ø¯ L.R≈éjG ö@KjqkÓ
> 5.T3»à3#j.RØ´) ö .K"ÓW%?‹.S≈E≈H!a.RÓE}ß‹ @K ÷qYÒ@SÖjé}ﬂH.S l‰%P6.Kg
> ‡¥çiY.Sá ïáÍx.S Á:û á@KË;„*y´@SYl‰§dâ@S3Æyˆû"@K%‡Øπ“p.S« v˙ƒ˜@RıkÛ
> ﬁª.JqT~Fˆî.S˙> ˝·ê@Rﬁã k˘[@J0=Ö Ç¸@SôÏ’æN’@S ˇs∫F.J3¢Ò§ÿ @Súö˘æè @R
> M!„µ.M 3¿}`˝.Sgm:] .R1 , √@Lª&C!õn.Sú?^€E*.Q¬ ù≠ @MN/
> 0∂Ø.S»'zb¸"@QÆÅ{Ô√i.M§p8|È@S^ ˚ Û @QÇ¯ËØ’2.M \1* Ê@Sbo*-ô±@QÅ]¢ àT.LÉ
> ‚Û7‚.SvF[*¬é.Q)∏K1-[@MQ ~ãºé@SE¬Å%·W.P˚ì
> Å…..M)bãπz#.S≥QˆÀ%U.Q G|˚L!.M #j.@S~ÀlBöÂ@Q'ˇ`JΩÕ@N ›‰•'r.S¢zOuEÑ@PˆG+Fä
> .N$≠\±,ª.S£˚)S·.Qôh ÒGï@M: ôŒ˛8.R»DZIl @Qãî◊Ï 8.LœΩç dK.RÔñ 1∫ @Qøâu
> áí.Mœ®"í±0.S π
> aÎé.QÃq &Ö.N Z•ÿr*.Rôµ¡¿o.Q€ø&Í‚È@N ¸>T %.Rkdºﬂ‹»@Q™–YçÜi.Mﬁ 2èÀ
> .Rò6Äº Ê.Q„»Ç¸ËD.N∆ù µü@Rƒ™RHŸf.R `ÍßKg.Nj˙'Yp.RW“Vø¯•@QÙ˙
> §#C.N^L^£À.R©√’≠ı≈.Q¶ﬁ ö\…@O˚∑@_d.R}—* öH.R0 öOv.M¨\áÓ8y.R2 Ò÷#ú@R<Ã≥
> -.MäkP{?W.R∫†cTd≥.Rh’ÌC86.MÑU¥wí—@R˜Ñù¶/U.R[}~
> ñ&.M¶À(∂Ä”.R™ª“f€à@R∏Cü⁄J∂@M$c”Y˝?.Rwäæ•– @R‹*¨‘Îü@Mbé⁄◊Ò5.R˝(Ï–~ê@RÓ ¢‡¶
> .M(¸ÿˇ .S 3Y ƒó@R˘ ÍÚl @MÆ'xm˜v.S/r.\"@R»J]Öh @LÏÙT '
> .R¯Çl∆Dy.SE&x 6Ù@LÕy◊A @RﬂÜe7°Ñ@S;ËZ˘Î˙@LL}ÓÈo¡@RÃx:&a$.SnôÍ|OÑ@M
> u¿ÀÙÒ.SPµy.a:.SpÇ0 … @Løè-£<3.STòÊú @S∫Ñ.x…í@LÇµB0M™@Sëè è¨Ü@SFäoû≤ @LÎ
> √üi.Rç˜ÈÖ}⁄.R•ÕÅ
> ·.Lk†m5Ωe.RP #˛[|.RÃ9)</‰.L.≤= –•.R∏ubÑ”Û@Rhî"zg @L 2—·©‹@RÏ& ¨—X.RN
> b4ÿ@LPY_t^7.R£û›´R∞@RLçÑëæı@Kg ¬£Úè@Rü ¥Œ–Ö@RÑˆ@ ≠€@K „≈‚ C.RÎ$◊x&y.R È M
> ¥@K s∆ä ˝@RÚdô í@Q€ã„A[Ω@Ku «Áä™@R“Ü"m«T.QÔUµ {A.Jl]”ª È@R¡^‡3xÏ@R$
> qª0W.J àR!7™@S ‡ü¨á@QÀ§∂¥éØ@J2´ñp ¿@RúBç "†@Qƒ 7®÷s.JvÃÁtÆE.SBL/Ïsˇ@R.0åπ¡Â@K
> ﬂ<Gn .SB˜öâG @RhÏƒÁ
> 2.Jüã>h¯F.SK…Iküd.Rh˜'ú(ﬁ@KÄ(N‚ ∆@Séü_9èk.R yÁ–ø]@K Õë1.Sä1u¬Ú@QŸ
> ﬂàf‘.Jô—òõ“”.S…√®„ƒÙ.R&Î~áÄX.J˛·ö$ﬁ-.Sê∞ØJ—°@Q€tÙW3 @K|¶êﬁs)@RLF *§ @R
> T≤f—.K`Iô¨ L.R *≥iˆ.R1Î-!
> 4.JÆ)“ È@R:“ﬂ%
> ñ.Q‰∞µ°S¯.K◊Ñr›„¯@Rg«œB
> Õ.QÿIzÙ
>
> ________________________________________________________________________
>
>
> Ryan S Czarny
> BMB PhD Candidate - Ho Lab
> Committee of University Programs - GSC Rep
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7CRyan.Czarny%40colostate.edu%7C49c413012f1d40655e4d08d7e0a06f53%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C637224851971424420&sdata=eLvx2f0Bv8z15v1svHUQq5QdpWuDsRaCEgkHLA3W17U%3D&reserved=0
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7CRyan.Czarny%40colostate.edu%7C49c413012f1d40655e4d08d7e0a06f53%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C637224851971424420&sdata=eLvx2f0Bv8z15v1svHUQq5QdpWuDsRaCEgkHLA3W17U%3D&reserved=0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 14 2020 - 12:30:01 PDT